ENST00000656751.1:n.85+20403T>C

Variant names:

• chr6-30764277-T-C
• rs3129975
• ENST00000656751.1:n.85+20403T>C

Variant summary

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

The ENST00000656751.1(HCG20):​n.85+20403T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,016 control chromosomes in the GnomAD database, including 2,349 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 0.17 (2349 hom., cov: 31)
• Consequence: HCG20 ENST00000656751.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660

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=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HCG20	ENST00000656751.1	n.85+20403T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25296 AN: 151898 Hom.: 2350 Cov.: 31

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.0756

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.166 AC: 25303 AN: 152016 Hom.: 2349 Cov.: 31 AF XY: 0.160 AC XY: 11920 AN XY: 74298

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.0756

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.222

Gnomad4 OTH AF: 0.149

Alfa AF: 0.197 Hom.: 3082

Bravo AF: 0.162

Asia WGS AF: 0.126 AC: 441 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	8.9
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3129975; hg19: chr6-30732054;