rs9263871

chr6-31202751-A-Gchr6-31202751-A-T

Variant summary

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

The NR_026791.1(HCG27):n.503A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 505,100 control chromosomes in the GnomAD database, including 35,456 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 0.36 (10214 hom., cov: 32)
  • Exomes 𝑓: 0.37 (25242 hom.)
• Consequence: HCG27 NR_026791.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59

Genes affected

HCG27 (HGNC:27366): (HLA complex group 27)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HCG27	NR_026791.1	n.503A>G		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HCG27	ENST00000383331.4	n.503A>G		non_coding_transcript_exon_variant	2/2	1

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54667 AN: 151822 Hom.: 10197 Cov.: 32

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.393

GnomAD3 exomes AF: 0.391 AC: 86860 AN: 222144 Hom.: 17808 AF XY: 0.383 AC XY: 46858 AN XY: 122360

Gnomad AFR exome AF: 0.304

Gnomad AMR exome AF: 0.507

Gnomad ASJ exome AF: 0.438

Gnomad EAS exome AF: 0.526

Gnomad SAS exome AF: 0.292

Gnomad FIN exome AF: 0.470

Gnomad NFE exome AF: 0.359

Gnomad OTH exome AF: 0.385

GnomAD4 exome AF: 0.368 AC: 130093 AN: 353160 Hom.: 25242 Cov.: 0 AF XY: 0.360 AC XY: 72755 AN XY: 202256

Gnomad4 AFR exome AF: 0.304

Gnomad4 AMR exome AF: 0.505

Gnomad4 ASJ exome AF: 0.429

Gnomad4 EAS exome AF: 0.516

Gnomad4 SAS exome AF: 0.295

Gnomad4 FIN exome AF: 0.454

Gnomad4 NFE exome AF: 0.352

Gnomad4 OTH exome AF: 0.355

GnomAD4 genome AF: 0.360 AC: 54707 AN: 151940 Hom.: 10214 Cov.: 32 AF XY: 0.367 AC XY: 27274 AN XY: 74258

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.462

Gnomad4 ASJ AF: 0.445

Gnomad4 EAS AF: 0.504

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.345

Gnomad4 OTH AF: 0.397

Alfa AF: 0.355 Hom.: 16702

Bravo AF: 0.362

Asia WGS AF: 0.385 AC: 1339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	3.7
Dann	Benign	0.69

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs9263871; hg19: chr6-31170528; COSMIC: COSV67271705;