chr6-29929222-C-G

Variant names:

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

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>G 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: 24)
• 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=-0.99).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HLA-K		n.29929222C>G		intragenic_variant
LOC124901298	XR_007059541.1	n.814-485G>C		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>G		non_coding_transcript_exon_variant	Exon 6 of 6	6
ENSG00000310496	ENST00000850440.1	n.500C>G		non_coding_transcript_exon_variant	Exon 4 of 5
ENSG00000310496	ENST00000850441.1	n.438C>G		non_coding_transcript_exon_variant	Exon 4 of 5

Frequencies

GnomAD3 genomes Cov.: 24

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 24

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	-0.99
CADD	Benign	4.7
DANN	Benign	0.47
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;