2-118985035-G-T

Variant names:

• chr2-118985035-G-T
• rs3731611
• NM_006770.4:c.1063+2625G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006770.4(MARCO):​c.1063+2625G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 152,060 control chromosomes in the GnomAD database, including 2,219 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 0.14 (2219 hom., cov: 32)
• Consequence: MARCO NM_006770.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130
• Publications: 3 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006770.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MARCO	NM_006770.4	MANE Select	c.1063+2625G>T		intron	N/A	NP_006761.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MARCO	ENST00000327097.5	TSL:1 MANE Select	c.1063+2625G>T		intron	N/A	ENSP00000318916.4
	MARCO	ENST00000874357.1		c.1063+2625G>T		intron	N/A	ENSP00000544416.1
	MARCO	ENST00000958830.1		c.1063+2625G>T		intron	N/A	ENSP00000628889.1

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21518 AN: 151942 Hom.: 2220 Cov.: 32

Gnomad AFR AF: 0.0401

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.145

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.142 AC: 21520 AN: 152060 Hom.: 2219 Cov.: 32 AF XY: 0.142 AC XY: 10581 AN XY: 74320

African (AFR) AF: 0.0401 AC: 1664 AN: 41512

American (AMR) AF: 0.177 AC: 2706 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 498 AN: 3468

East Asian (EAS) AF: 0.504 AC: 2589 AN: 5138

South Asian (SAS) AF: 0.153 AC: 737 AN: 4808

European-Finnish (FIN) AF: 0.143 AC: 1509 AN: 10582

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11088 AN: 67972

Other (OTH) AF: 0.146 AC: 307 AN: 2104

Alfa AF: 0.153 Hom.: 1710

Bravo AF: 0.146

Asia WGS AF: 0.310 AC: 1075 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.4
DANN	Benign	0.45
PhyloP100		-0.013
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

Other links and lift over

dbSNP: rs3731611; hg19: chr2-119742611;