chr2-118969706-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006770.4(MARCO):​c.200-408C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,174 control chromosomes in the GnomAD database, including 1,387 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.13 ( 1387 hom., cov: 33)

Consequence

MARCO
NM_006770.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.37

Publications

4 publications found
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 was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MARCONM_006770.4 linkc.200-408C>T intron_variant Intron 2 of 16 ENST00000327097.5 NP_006761.1 Q9UEW3-1Q4ZG40
MARCOXM_011512082.3 linkc.200-408C>T intron_variant Intron 2 of 16 XP_011510384.1 Q9UEW3-1Q4ZG40
MARCOXM_011512083.4 linkc.98-4627C>T intron_variant Intron 1 of 13 XP_011510385.1
MARCOXM_017005171.3 linkc.200-408C>T intron_variant Intron 2 of 8 XP_016860660.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MARCOENST00000327097.5 linkc.200-408C>T intron_variant Intron 2 of 16 1 NM_006770.4 ENSP00000318916.4 Q9UEW3-1
MARCOENST00000412481.1 linkc.-35-408C>T intron_variant Intron 3 of 3 4 ENSP00000409192.1 C9JKT8

Frequencies

GnomAD3 genomes
AF:
0.128
AC:
19497
AN:
152056
Hom.:
1387
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0900
Gnomad AMI
AF:
0.0965
Gnomad AMR
AF:
0.166
Gnomad ASJ
AF:
0.165
Gnomad EAS
AF:
0.242
Gnomad SAS
AF:
0.269
Gnomad FIN
AF:
0.139
Gnomad MID
AF:
0.143
Gnomad NFE
AF:
0.121
Gnomad OTH
AF:
0.120
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.128
AC:
19512
AN:
152174
Hom.:
1387
Cov.:
33
AF XY:
0.132
AC XY:
9834
AN XY:
74378
show subpopulations
African (AFR)
AF:
0.0899
AC:
3735
AN:
41530
American (AMR)
AF:
0.167
AC:
2550
AN:
15292
Ashkenazi Jewish (ASJ)
AF:
0.165
AC:
572
AN:
3472
East Asian (EAS)
AF:
0.242
AC:
1252
AN:
5170
South Asian (SAS)
AF:
0.268
AC:
1292
AN:
4824
European-Finnish (FIN)
AF:
0.139
AC:
1471
AN:
10582
Middle Eastern (MID)
AF:
0.147
AC:
43
AN:
292
European-Non Finnish (NFE)
AF:
0.121
AC:
8249
AN:
67984
Other (OTH)
AF:
0.123
AC:
260
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
879
1758
2638
3517
4396
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
234
468
702
936
1170
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.129
Hom.:
161
Bravo
AF:
0.128
Asia WGS
AF:
0.284
AC:
989
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.065
DANN
Benign
0.68
PhyloP100
-2.4
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs2278588; hg19: chr2-119727282; API