2-118967393-C-T

Variant names:

• chr2-118967393-C-T
• rs7559955
• NM_006770.4:c.98-1767C>T

Variant summary

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

The ENST00000327097.5(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 ENST00000327097.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 6 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000327097.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MARCO	NM_006770.4	MANE Select	c.98-1767C>T		intron	N/A	NP_006761.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MARCO	ENST00000327097.5	TSL:1 MANE Select	c.98-1767C>T		intron	N/A	ENSP00000318916.4
	MARCO	ENST00000412481.1	TSL:4	c.-137-1767C>T		intron	N/A	ENSP00000409192.1

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

African (AFR) AF: 0.331 AC: 13698 AN: 41434

American (AMR) AF: 0.0995 AC: 1521 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 390 AN: 3472

East Asian (EAS) AF: 0.219 AC: 1127 AN: 5138

South Asian (SAS) AF: 0.313 AC: 1500 AN: 4800

European-Finnish (FIN) AF: 0.156 AC: 1648 AN: 10578

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7604 AN: 68008

Other (OTH) AF: 0.162 AC: 341 AN: 2106

Alfa AF: 0.131 Hom.: 5992

Bravo AF: 0.181

Asia WGS AF: 0.232 AC: 806 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.23
DANN	Benign	0.32
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: rs7559955; hg19: chr2-119724969;