rs389600

Variant names:

• chr6-29929222-C-A
• rs389600
• ENST00000430151.2:n.1036C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-29929222-C-A
• chr6-29929222-C-G
• chr6-29929222-C-T

Variant summary

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

The ENST00000430151.2(HLA-K):​n.1036C>A 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 0.00000625 in 480,064 control chromosomes in the GnomAD database, including 1 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 0.0000078 (0 hom., cov: 24)
  • Exomes 𝑓: 0.0000057 (1 hom.)
• Consequence: HLA-K ENST00000430151.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -7.51
• Publications: 11 publications found

Genes affected

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

ENSG00000310496 (HGNC:):

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=-0.97).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HLA-K		n.29929222C>A		intragenic_variant
LOC124901298	XR_007059541.1	n.814-485G>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HLA-K	ENST00000430151.2	n.1036C>A		non_coding_transcript_exon_variant	Exon 6 of 6	6
ENSG00000310496	ENST00000850440.1	n.500C>A		non_coding_transcript_exon_variant	Exon 4 of 5
ENSG00000310496	ENST00000850441.1	n.438C>A		non_coding_transcript_exon_variant	Exon 4 of 5

Frequencies

GnomAD3 genomes AF: 0.00000777 AC: 1 AN: 128700 Hom.: 0 Cov.: 24

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000161

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00000569 AC: 2 AN: 351364 Hom.: 1 Cov.: 0 AF XY: 0.0000102 AC XY: 2 AN XY: 196968

African (AFR) AF: 0.00 AC: 0 AN: 9378

American (AMR) AF: 0.0000776 AC: 2 AN: 25764

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9548

East Asian (EAS) AF: 0.00 AC: 0 AN: 14090

South Asian (SAS) AF: 0.00 AC: 0 AN: 53470

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 29706

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2694

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 189950

Other (OTH) AF: 0.00 AC: 0 AN: 16764

GnomAD4 genome AF: 0.00000777 AC: 1 AN: 128700 Hom.: 0 Cov.: 24 AF XY: 0.0000162 AC XY: 1 AN XY: 61892

African (AFR) AF: 0.00 AC: 0 AN: 32806

American (AMR) AF: 0.00 AC: 0 AN: 11804

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3112

East Asian (EAS) AF: 0.00 AC: 0 AN: 3854

South Asian (SAS) AF: 0.00 AC: 0 AN: 3656

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8602

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 272

European-Non Finnish (NFE) AF: 0.0000161 AC: 1 AN: 62012

Other (OTH) AF: 0.00 AC: 0 AN: 1742

Alfa AF: 0.00 Hom.: 104

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.83
DANN	Benign	0.62
PhyloP100		-7.5

Splicing

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

Other links and lift over

dbSNP: rs389600; hg19: chr6-29896999;