rs1632902

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr6-29929635-G-A
• chr6-29929635-G-C
• chr6-29929635-G-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000850441.1(ENSG00000310496):​n.683G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.9
DANN	Benign	0.35
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;