rs2894181

Variant names:

• chr6-31206750-A-G
• rs2894181
• ENST00000755328.1:n.161+2640A>G

Your query was ambiguous. Multiple possible variants found:

• chr6-31206750-A-G
• chr6-31206750-A-T

Variant summary

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

The ENST00000755328.1(HCG27):​n.161+2640A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 151,956 control chromosomes in the GnomAD database, including 17,286 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 0.47 (17286 hom., cov: 30)
• Consequence: HCG27 ENST00000755328.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 29 publications found

Genes affected

HCG27 (HGNC:27366): (HLA complex group 27)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755328.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCG27	ENST00000755328.1		n.161+2640A>G		intron	N/A
	HCG27	ENST00000755329.1		n.160-1664A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72084 AN: 151838 Hom.: 17273 Cov.: 30

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.475 AC: 72125 AN: 151956 Hom.: 17286 Cov.: 30 AF XY: 0.478 AC XY: 35513 AN XY: 74258

African (AFR) AF: 0.444 AC: 18386 AN: 41450

American (AMR) AF: 0.527 AC: 8047 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1783 AN: 3468

East Asian (EAS) AF: 0.392 AC: 2031 AN: 5176

South Asian (SAS) AF: 0.406 AC: 1957 AN: 4824

European-Finnish (FIN) AF: 0.571 AC: 6020 AN: 10540

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.475 AC: 32290 AN: 67932

Other (OTH) AF: 0.500 AC: 1055 AN: 2112

Alfa AF: 0.474 Hom.: 50849

Bravo AF: 0.476

Asia WGS AF: 0.476 AC: 1655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.54
PhyloP100		-1.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2894181;

hg19: chr6-31174527;