rs2077344

Variant names:

• chr2-118942520-T-A
• rs2077344
• NM_006770.4:c.97+123T>A

Your query was ambiguous. Multiple possible variants found:

• chr2-118942520-T-A
• chr2-118942520-T-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_006770.4(MARCO):​c.97+123T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MARCO NM_006770.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.698
• Publications: 4 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MARCO	NM_006770.4	c.97+123T>A		intron_variant	Intron 1 of 16	ENST00000327097.5	NP_006761.1
MARCO	XM_011512082.3	c.97+123T>A		intron_variant	Intron 1 of 16		XP_011510384.1
MARCO	XM_011512083.4	c.97+123T>A		intron_variant	Intron 1 of 13		XP_011510385.1
MARCO	XM_017005171.3	c.97+123T>A		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.97+123T>A		intron_variant	Intron 1 of 16	1	NM_006770.4	ENSP00000318916.4
MARCO	ENST00000412481.1	c.-271+123T>A		intron_variant	Intron 1 of 3	4		ENSP00000409192.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 560404 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 295874

African (AFR) AF: 0.00 AC: 0 AN: 14854

American (AMR) AF: 0.00 AC: 0 AN: 27882

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 16240

East Asian (EAS) AF: 0.00 AC: 0 AN: 31220

South Asian (SAS) AF: 0.00 AC: 0 AN: 53504

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 38788

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3688

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 344510

Other (OTH) AF: 0.00 AC: 0 AN: 29718

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.1
DANN	Benign	0.69
PhyloP100		-0.70
PromoterAI		0.0085	Neutral

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: rs2077344; hg19: chr2-119700096;