rs13214831

Variant names:

• chr6-30763728-G-A
• rs13214831
• ENST00000656751.1:n.85+19854G>A

Variant summary

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

The ENST00000656751.1(HCG20):​n.85+19854G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,196 control chromosomes in the GnomAD database, including 3,131 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 (3131 hom., cov: 32)
• Consequence: HCG20 ENST00000656751.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123
• Publications: 22 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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.388 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+19854G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26227 AN: 152078 Hom.: 3123 Cov.: 32

Gnomad AFR AF: 0.0692

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.172 AC: 26242 AN: 152196 Hom.: 3131 Cov.: 32 AF XY: 0.179 AC XY: 13287 AN XY: 74412

African (AFR) AF: 0.0691 AC: 2871 AN: 41528

American (AMR) AF: 0.334 AC: 5109 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1398 AN: 3472

East Asian (EAS) AF: 0.370 AC: 1908 AN: 5162

South Asian (SAS) AF: 0.403 AC: 1942 AN: 4822

European-Finnish (FIN) AF: 0.114 AC: 1210 AN: 10598

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11103 AN: 68010

Other (OTH) AF: 0.202 AC: 427 AN: 2112

Alfa AF: 0.175 Hom.: 8437

Bravo AF: 0.183

Asia WGS AF: 0.369 AC: 1286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.2
DANN	Benign	0.35
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs13214831; hg19: chr6-30731505;