ENST00000383331.4:n.503A>G

Variant names:

• chr6-31202751-A-G
• rs9263871
• ENST00000383331.4:n.503A>G

Variant summary

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

The ENST00000383331.4(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 ENST00000383331.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• Publications: 56 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000383331.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCG27	NR_026791.1		n.503A>G		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCG27	ENST00000383331.4	TSL:1	n.503A>G		non_coding_transcript_exon	Exon 2 of 2
	HCG27	ENST00000638546.2	TSL:1	n.546A>G		non_coding_transcript_exon	Exon 2 of 2
	HCG27	ENST00000415276.2	TSL:3	n.421A>G		non_coding_transcript_exon	Exon 2 of 2

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

GnomAD2 exomes AF: 0.391 AC: 86860 AN: 222144 AF XY: 0.383

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 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

African (AFR) AF: 0.304 AC: 3066 AN: 10098

American (AMR) AF: 0.505 AC: 17643 AN: 34938

Ashkenazi Jewish (ASJ) AF: 0.429 AC: 4509 AN: 10506

East Asian (EAS) AF: 0.516 AC: 6700 AN: 12980

South Asian (SAS) AF: 0.295 AC: 19320 AN: 65388

European-Finnish (FIN) AF: 0.454 AC: 7479 AN: 16478

Middle Eastern (MID) AF: 0.318 AC: 879 AN: 2766

European-Non Finnish (NFE) AF: 0.352 AC: 64844 AN: 184078

Other (OTH) AF: 0.355 AC: 5653 AN: 15928

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

African (AFR) AF: 0.303 AC: 12540 AN: 41444

American (AMR) AF: 0.462 AC: 7047 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.445 AC: 1542 AN: 3462

East Asian (EAS) AF: 0.504 AC: 2600 AN: 5160

South Asian (SAS) AF: 0.295 AC: 1423 AN: 4816

European-Finnish (FIN) AF: 0.464 AC: 4892 AN: 10550

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.345 AC: 23442 AN: 67946

Other (OTH) AF: 0.397 AC: 835 AN: 2104

Alfa AF: 0.355 Hom.: 29807

Bravo AF: 0.362

Asia WGS AF: 0.385 AC: 1339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.7
DANN	Benign	0.69
PhyloP100		-1.6

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9263871;

hg19: chr6-31170528;

COSMIC: COSV67271705;