NM_006770.4:c.1207+160C>T

Variant names:

• chr2-118992035-C-T
• rs4848530
• NM_006770.4:c.1207+160C>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.1207+160C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 152,128 control chromosomes in the GnomAD database, including 10,622 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 0.35 (10622 hom., cov: 33)
• Consequence: MARCO NM_006770.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.759
• Publications: 8 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]

LOC124906072 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.462 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MARCO	NM_006770.4	MANE Select	c.1207+160C>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.1207+160C>T		intron	N/A	ENSP00000318916.4
	MARCO	ENST00000874357.1		c.1294+160C>T		intron	N/A	ENSP00000544416.1
	MARCO	ENST00000958830.1		c.1249+160C>T		intron	N/A	ENSP00000628889.1

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52803 AN: 152010 Hom.: 10619 Cov.: 33

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.347 AC: 52816 AN: 152128 Hom.: 10622 Cov.: 33 AF XY: 0.344 AC XY: 25589 AN XY: 74372

African (AFR) AF: 0.142 AC: 5881 AN: 41540

American (AMR) AF: 0.341 AC: 5220 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1690 AN: 3468

East Asian (EAS) AF: 0.262 AC: 1351 AN: 5156

South Asian (SAS) AF: 0.311 AC: 1501 AN: 4824

European-Finnish (FIN) AF: 0.412 AC: 4355 AN: 10572

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.466 AC: 31663 AN: 67962

Other (OTH) AF: 0.379 AC: 799 AN: 2106

Alfa AF: 0.419 Hom.: 33582

Bravo AF: 0.337

Asia WGS AF: 0.312 AC: 1086 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	0.058
DANN	Benign	0.78
PhyloP100		-0.76
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs4848530; hg19: chr2-119749611; COSMIC: COSV59058375; COSMIC: COSV59058375;