6-29929222-C-T

Variant names:

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

Variant summary

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

The ENST00000430151.2(HLA-K):​n.1036C>T 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 0.135 in 479,312 control chromosomes in the GnomAD database, including 8,761 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 0.14 (2399 hom., cov: 24)
  • Exomes 𝑓: 0.13 (6362 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes AF: 0.137 AC: 17581 AN: 128544 Hom.: 2398 Cov.: 24

Gnomad AFR AF: 0.0873

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.0937

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.0223

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.0875

Gnomad MID AF: 0.147

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.131

GnomAD4 exome AF: 0.134 AC: 47086 AN: 350680 Hom.: 6362 Cov.: 0 AF XY: 0.136 AC XY: 26829 AN XY: 196562

African (AFR) AF: 0.0840 AC: 787 AN: 9370

American (AMR) AF: 0.0654 AC: 1685 AN: 25748

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 1247 AN: 9516

East Asian (EAS) AF: 0.0119 AC: 168 AN: 14088

South Asian (SAS) AF: 0.144 AC: 7697 AN: 53370

European-Finnish (FIN) AF: 0.0799 AC: 2368 AN: 29634

Middle Eastern (MID) AF: 0.117 AC: 314 AN: 2692

European-Non Finnish (NFE) AF: 0.161 AC: 30565 AN: 189542

Other (OTH) AF: 0.135 AC: 2255 AN: 16720

GnomAD4 genome AF: 0.137 AC: 17579 AN: 128632 Hom.: 2399 Cov.: 24 AF XY: 0.131 AC XY: 8127 AN XY: 61910

African (AFR) AF: 0.0872 AC: 2865 AN: 32864

American (AMR) AF: 0.0935 AC: 1105 AN: 11816

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 446 AN: 3110

East Asian (EAS) AF: 0.0224 AC: 86 AN: 3842

South Asian (SAS) AF: 0.162 AC: 591 AN: 3640

European-Finnish (FIN) AF: 0.0875 AC: 751 AN: 8584

Middle Eastern (MID) AF: 0.146 AC: 37 AN: 254

European-Non Finnish (NFE) AF: 0.183 AC: 11313 AN: 61936

Other (OTH) AF: 0.131 AC: 229 AN: 1748

Alfa AF: 0.0761 Hom.: 104

Asia WGS AF: 0.0880 AC: 276 AN: 3114

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.6
DANN	Benign	0.74
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;