rs3129975

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr6-30764277-T-C
• chr6-30764277-T-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 21 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=-0.76).
• 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

African (AFR) AF: 0.109 AC: 4527 AN: 41434

American (AMR) AF: 0.129 AC: 1972 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 504 AN: 3470

East Asian (EAS) AF: 0.0756 AC: 392 AN: 5184

South Asian (SAS) AF: 0.160 AC: 771 AN: 4816

European-Finnish (FIN) AF: 0.149 AC: 1569 AN: 10560

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.222 AC: 15059 AN: 67976

Other (OTH) AF: 0.149 AC: 314 AN: 2110

Alfa AF: 0.192 Hom.: 4511

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
PhyloP100		-0.066

Splicing

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

Other links and lift over

dbSNP: rs3129975; hg19: chr6-30732054;