2-118967393-C-T

Position:

• chr2-118967393-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.98-1767C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 152,034 control chromosomes in the GnomAD database, including 3,412 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 0.18 (3412 hom., cov: 32)
• Consequence: MARCO NM_006770.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MARCO	NM_006770.4	c.98-1767C>T		intron_variant		ENST00000327097.5	NP_006761.1
MARCO	XM_011512082.3	c.98-1767C>T		intron_variant			XP_011510384.1
MARCO	XM_011512083.4	c.98-6940C>T		intron_variant			XP_011510385.1
MARCO	XM_017005171.3	c.98-1767C>T		intron_variant			XP_016860660.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MARCO	ENST00000327097.5	c.98-1767C>T		intron_variant		1	NM_006770.4	ENSP00000318916	P1
MARCO	ENST00000412481.1	c.-137-1767C>T		intron_variant		4		ENSP00000409192

Frequencies

GnomAD3 genomes AF: 0.184 AC: 27934 AN: 151916 Hom.: 3402 Cov.: 32

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.0996

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.184 AC: 27983 AN: 152034 Hom.: 3412 Cov.: 32 AF XY: 0.187 AC XY: 13918 AN XY: 74312

Gnomad4 AFR AF: 0.331

Gnomad4 AMR AF: 0.0995

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.219

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.162

Alfa AF: 0.115 Hom.: 1946

Bravo AF: 0.181

Asia WGS AF: 0.232 AC: 806 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.23
DANN	Benign	0.32

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: rs7559955; hg19: chr2-119724969;