chr2-118960452-A-G

Variant names:

• chr2-118960452-A-G
• rs4491733
• NM_006770.4:c.98-8708A>G

Variant summary

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

The NM_006770.4(MARCO):​c.98-8708A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 151,892 control chromosomes in the GnomAD database, including 12,467 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 0.37 (12467 hom., cov: 32)
• Consequence: MARCO NM_006770.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 25 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MARCO	NM_006770.4	c.98-8708A>G		intron_variant	Intron 1 of 16	ENST00000327097.5	NP_006761.1
MARCO	XM_011512082.3	c.98-8708A>G		intron_variant	Intron 1 of 16		XP_011510384.1
MARCO	XM_011512083.4	c.98-13881A>G		intron_variant	Intron 1 of 13		XP_011510385.1
MARCO	XM_017005171.3	c.98-8708A>G		intron_variant	Intron 1 of 8		XP_016860660.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MARCO	ENST00000327097.5	c.98-8708A>G		intron_variant	Intron 1 of 16	1	NM_006770.4	ENSP00000318916.4
MARCO	ENST00000412481.1	c.-137-8708A>G		intron_variant	Intron 2 of 3	4		ENSP00000409192.1

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55719 AN: 151774 Hom.: 12438 Cov.: 32

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.367 AC: 55804 AN: 151892 Hom.: 12467 Cov.: 32 AF XY: 0.373 AC XY: 27712 AN XY: 74236

African (AFR) AF: 0.613 AC: 25387 AN: 41438

American (AMR) AF: 0.285 AC: 4347 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 962 AN: 3470

East Asian (EAS) AF: 0.462 AC: 2374 AN: 5138

South Asian (SAS) AF: 0.581 AC: 2802 AN: 4820

European-Finnish (FIN) AF: 0.294 AC: 3096 AN: 10530

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.234 AC: 15877 AN: 67924

Other (OTH) AF: 0.320 AC: 675 AN: 2110

Alfa AF: 0.282 Hom.: 18187

Bravo AF: 0.373

Asia WGS AF: 0.524 AC: 1818 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.5
DANN	Benign	0.59
PhyloP100		-1.2
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: rs4491733; hg19: chr2-119718028;