rs3131036

Variant names:

• chr6-30760513-G-A
• rs3131036
• ENST00000656751.1:n.85+16639G>A

Variant summary

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

The ENST00000656751.1(HCG20):​n.85+16639G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 151,880 control chromosomes in the GnomAD database, including 7,076 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 0.29 (7076 hom., cov: 32)
• Consequence: HCG20 ENST00000656751.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.732
• Publications: 20 publications found

Genes affected

HCG20 (HGNC:31334): (HLA complex group 20)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656751.1. 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
	HCG20	ENST00000656751.1		n.85+16639G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44121 AN: 151762 Hom.: 7056 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.291 AC: 44172 AN: 151880 Hom.: 7076 Cov.: 32 AF XY: 0.282 AC XY: 20900 AN XY: 74216

African (AFR) AF: 0.423 AC: 17492 AN: 41390

American (AMR) AF: 0.265 AC: 4051 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 761 AN: 3472

East Asian (EAS) AF: 0.135 AC: 696 AN: 5162

South Asian (SAS) AF: 0.172 AC: 828 AN: 4814

European-Finnish (FIN) AF: 0.163 AC: 1713 AN: 10520

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.262 AC: 17772 AN: 67938

Other (OTH) AF: 0.290 AC: 612 AN: 2110

Alfa AF: 0.276 Hom.: 21900

Bravo AF: 0.306

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.27
DANN	Benign	0.63
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs3131036; hg19: chr6-30728290;