chr6-29929635-G-C

Variant names:

• chr6-29929635-G-C
• rs1632902
• ENST00000850441.1:n.683G>C

Variant summary

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

The ENST00000850441.1(ENSG00000310496):​n.683G>C 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 0.295 in 146,398 control chromosomes in the GnomAD database, including 9,615 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 (9615 hom., cov: 30)
• Consequence: ENSG00000310496 ENST00000850441.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.547
• Publications: 4 publications found

Genes affected

ENSG00000310496 (HGNC:):

HLA-K (HGNC:4969): (major histocompatibility complex, class I, K (pseudogene))

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HLA-K		n.29929635G>C		intragenic_variant
LOC124901298	XR_007059541.1	n.814-898C>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000310496	ENST00000850441.1	n.683G>C		non_coding_transcript_exon_variant	Exon 5 of 5
ENSG00000310496	ENST00000850442.1	n.622G>C		non_coding_transcript_exon_variant	Exon 5 of 5
ENSG00000310496	ENST00000850443.1	n.1370G>C		non_coding_transcript_exon_variant	Exon 8 of 8

Frequencies

GnomAD3 genomes AF: 0.295 AC: 43084 AN: 146288 Hom.: 9598 Cov.: 30

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.372

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.295 AC: 43147 AN: 146398 Hom.: 9615 Cov.: 30 AF XY: 0.291 AC XY: 20746 AN XY: 71394

African (AFR) AF: 0.260 AC: 10301 AN: 39558

American (AMR) AF: 0.305 AC: 4366 AN: 14318

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1577 AN: 3378

East Asian (EAS) AF: 0.245 AC: 1152 AN: 4704

South Asian (SAS) AF: 0.403 AC: 1801 AN: 4470

European-Finnish (FIN) AF: 0.171 AC: 1752 AN: 10240

Middle Eastern (MID) AF: 0.378 AC: 105 AN: 278

European-Non Finnish (NFE) AF: 0.319 AC: 21249 AN: 66552

Other (OTH) AF: 0.310 AC: 624 AN: 2010

Alfa AF: 0.110 Hom.: 235

Asia WGS AF: 0.319 AC: 994 AN: 3116

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.24
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs1632902; hg19: chr6-29897412; COSMIC: COSV69848011;