chr6-30763728-G-A

Position:

• chr6-30763728-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+19854G>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 0.172 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123

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=-0.86).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HCG20	ENST00000656751.1	n.85+19854G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0691

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.403

Gnomad4 EAS AF: 0.370

Gnomad4 SAS AF: 0.403

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.202

Alfa AF: 0.182 Hom.: 2965

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13214831; hg19: chr6-30731505;