rs9262176

Positions:

• chr6-30763553-C-T

Variant summary

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

The ENST00000656751.1(HCG20):​n.85+19679C>T 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 0.0866 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.622

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.205 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+19679C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.208

Gnomad4 AMR AF: 0.0856

Gnomad4 ASJ AF: 0.0839

Gnomad4 EAS AF: 0.0176

Gnomad4 SAS AF: 0.0430

Gnomad4 FIN AF: 0.00236

Gnomad4 NFE AF: 0.0348

Gnomad4 OTH AF: 0.105

Alfa AF: 0.0438 Hom.: 389

Bravo AF: 0.100

Asia WGS AF: 0.0510 AC: 175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9262176; hg19: chr6-30731330;