ENST00000656751.1:n.85+19679C>T

Variant names:

• chr6-30763553-C-T
• rs9262176
• ENST00000656751.1:n.85+19679C>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+19679C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0866 in 152,038 control chromosomes in the GnomAD database, including 1,067 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 0.087 (1067 hom., cov: 30)
• Consequence: HCG20 ENST00000656751.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.622
• Publications: 13 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.205 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCG20	ENST00000656751.1		n.85+19679C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0866 AC: 13149 AN: 151920 Hom.: 1066 Cov.: 30

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0857

Gnomad ASJ AF: 0.0839

Gnomad EAS AF: 0.0173

Gnomad SAS AF: 0.0430

Gnomad FIN AF: 0.00236

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0348

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.0866 AC: 13170 AN: 152038 Hom.: 1067 Cov.: 30 AF XY: 0.0835 AC XY: 6209 AN XY: 74340

African (AFR) AF: 0.208 AC: 8637 AN: 41436

American (AMR) AF: 0.0856 AC: 1307 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0839 AC: 291 AN: 3470

East Asian (EAS) AF: 0.0176 AC: 91 AN: 5178

South Asian (SAS) AF: 0.0430 AC: 207 AN: 4814

European-Finnish (FIN) AF: 0.00236 AC: 25 AN: 10588

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0348 AC: 2367 AN: 67976

Other (OTH) AF: 0.105 AC: 221 AN: 2110

Alfa AF: 0.0522 Hom.: 1628

Bravo AF: 0.100

Asia WGS AF: 0.0510 AC: 175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.40
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs9262176; hg19: chr6-30731330;