chr2-118969706-C-T

Position:

• chr2-118969706-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.37

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
MARCO	NM_006770.4	c.200-408C>T		intron_variant		ENST00000327097.5
MARCO	XM_011512082.3	c.200-408C>T		intron_variant
MARCO	XM_011512083.4	c.98-4627C>T		intron_variant
MARCO	XM_017005171.3	c.200-408C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MARCO	ENST00000327097.5	c.200-408C>T		intron_variant		1	NM_006770.4	P1
MARCO	ENST00000412481.1	c.-35-408C>T		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19497 AN: 152056 Hom.: 1387 Cov.: 33

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

Gnomad4 AFR AF: 0.0899

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.123

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

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

Other links and lift over

dbSNP: rs2278588; hg19: chr2-119727282;