rs6926530

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000656751.1(HCG20):​n.85+18616A>G variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.753

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HCG20	ENST00000656751.1	n.85+18616A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.0422

Gnomad4 ASJ AF: 0.0557

Gnomad4 EAS AF: 0.0794

Gnomad4 SAS AF: 0.0665

Gnomad4 FIN AF: 0.00617

Gnomad4 NFE AF: 0.0265

Gnomad4 OTH AF: 0.0674

Alfa AF: 0.0308 Hom.: 95

Bravo AF: 0.0784

Asia WGS AF: 0.0720 AC: 250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6926530; hg19: chr6-30730267;