rs3131036

chr6-30760513-G-A

Variant summary

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

The ENST00000656751.1(HCG20):n.85+16639G>A 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 0.291 in 151,880 control chromosomes in the GnomAD database, including 7,076 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 0.29 (7076 hom., cov: 32)
• Consequence: HCG20 ENST00000656751.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.732

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.417 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+16639G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44121 AN: 151762 Hom.: 7056 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.291 AC: 44172 AN: 151880 Hom.: 7076 Cov.: 32 AF XY: 0.282 AC XY: 20900 AN XY: 74216

Gnomad4 AFR AF: 0.423

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.290

Alfa AF: 0.264 Hom.: 7340

Bravo AF: 0.306

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.27
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3131036; hg19: chr6-30728290;