Menu
GeneBe

2-118942330-C-T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_006770.4(MARCO):c.30C>T(p.Asp10=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00293 in 1,613,504 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0020 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0030 ( 10 hom. )

Consequence

MARCO
NM_006770.4 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.138
Variant links:
Genes affected
MARCO (HGNC:6895): (macrophage receptor with collagenous structure) The protein encoded by this gene is a member of the class A scavenger receptor family and is part of the innate antimicrobial immune system. The protein may bind both Gram-negative and Gram-positive bacteria via an extracellular, C-terminal, scavenger receptor cysteine-rich (SRCR) domain. In addition to short cytoplasmic and transmembrane domains, there is an extracellular spacer domain and a long, extracellular collagenous domain. The protein may form a trimeric molecule by the association of the collagenous domains of three identical polypeptide chains. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 2-118942330-C-T is Benign according to our data. Variant chr2-118942330-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 718395.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.138 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAdExome at 2 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MARCONM_006770.4 linkuse as main transcriptc.30C>T p.Asp10= synonymous_variant 1/17 ENST00000327097.5
MARCOXM_011512082.3 linkuse as main transcriptc.30C>T p.Asp10= synonymous_variant 1/17
MARCOXM_011512083.4 linkuse as main transcriptc.30C>T p.Asp10= synonymous_variant 1/14
MARCOXM_017005171.3 linkuse as main transcriptc.30C>T p.Asp10= synonymous_variant 1/9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MARCOENST00000327097.5 linkuse as main transcriptc.30C>T p.Asp10= synonymous_variant 1/171 NM_006770.4 P1Q9UEW3-1
MARCOENST00000412481.1 linkuse as main transcriptc.-338C>T 5_prime_UTR_variant 1/44

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00195
AC:
297
AN:
152104
Hom.:
1
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000676
Gnomad AMI
AF:
0.0143
Gnomad AMR
AF:
0.00203
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000386
Gnomad SAS
AF:
0.000831
Gnomad FIN
AF:
0.000189
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00318
Gnomad OTH
AF:
0.000478
GnomAD3 exomes
AF:
0.00166
AC:
417
AN:
250722
Hom.:
2
AF XY:
0.00163
AC XY:
221
AN XY:
135502
show subpopulations
Gnomad AFR exome
AF:
0.000308
Gnomad AMR exome
AF:
0.00133
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00114
Gnomad FIN exome
AF:
0.000508
Gnomad NFE exome
AF:
0.00274
Gnomad OTH exome
AF:
0.00164
GnomAD4 exome
AF:
0.00303
AC:
4433
AN:
1461282
Hom.:
10
Cov.:
30
AF XY:
0.00299
AC XY:
2172
AN XY:
726956
show subpopulations
Gnomad4 AFR exome
AF:
0.000358
Gnomad4 AMR exome
AF:
0.00125
Gnomad4 ASJ exome
AF:
0.0000383
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00101
Gnomad4 FIN exome
AF:
0.000543
Gnomad4 NFE exome
AF:
0.00368
Gnomad4 OTH exome
AF:
0.00255
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00195
AC:
297
AN:
152222
Hom.:
1
Cov.:
32
AF XY:
0.00179
AC XY:
133
AN XY:
74432
show subpopulations
Gnomad4 AFR
AF:
0.000674
Gnomad4 AMR
AF:
0.00203
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000387
Gnomad4 SAS
AF:
0.000832
Gnomad4 FIN
AF:
0.000189
Gnomad4 NFE
AF:
0.00318
Gnomad4 OTH
AF:
0.000473
Alfa
AF:
0.00190
Hom.:
0
Bravo
AF:
0.00205
EpiCase
AF:
0.00262
EpiControl
AF:
0.00321

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingInvitaeMay 24, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.75
Cadd
Benign
4.0
Dann
Benign
0.21

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs80217020; hg19: chr2-119699906; API