rs6926530

Variant names:

• chr6-30762490-A-G
• rs6926530
• ENST00000656751.1:n.85+18616A>G

Your query was ambiguous. Multiple possible variants found:

• chr6-30762490-A-G
• chr6-30762490-A-T

Variant summary

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

The ENST00000656751.1(HCG20):​n.85+18616A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0711 in 151,488 control chromosomes in the GnomAD database, including 723 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 0.071 (723 hom., cov: 31)
• Consequence: HCG20 ENST00000656751.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.753
• Publications: 12 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.17 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+18616A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0711 AC: 10755 AN: 151364 Hom.: 722 Cov.: 31

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0422

Gnomad ASJ AF: 0.0557

Gnomad EAS AF: 0.0796

Gnomad SAS AF: 0.0666

Gnomad FIN AF: 0.00617

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0265

Gnomad OTH AF: 0.0690

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

GnomAD4 genome AF: 0.0711 AC: 10767 AN: 151488 Hom.: 723 Cov.: 31 AF XY: 0.0698 AC XY: 5170 AN XY: 74060

African (AFR) AF: 0.173 AC: 7164 AN: 41374

American (AMR) AF: 0.0422 AC: 639 AN: 15160

Ashkenazi Jewish (ASJ) AF: 0.0557 AC: 193 AN: 3468

East Asian (EAS) AF: 0.0794 AC: 405 AN: 5100

South Asian (SAS) AF: 0.0665 AC: 312 AN: 4690

European-Finnish (FIN) AF: 0.00617 AC: 65 AN: 10534

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0265 AC: 1800 AN: 67848

Other (OTH) AF: 0.0674 AC: 142 AN: 2108

Alfa AF: 0.0410 Hom.: 280

Bravo AF: 0.0784

Asia WGS AF: 0.0720 AC: 250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.44
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs6926530; hg19: chr6-30730267;