rs2517754

Positions:

• chr6-29928903-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000430151.2(HLA-K):​n.1000-283A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 145,534 control chromosomes in the GnomAD database, including 19,628 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 0.47 (19628 hom., cov: 29)
• Consequence: HLA-K ENST00000430151.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.529

Genes affected

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

LOC124901298 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901298	XR_007059541.1	n.814-166T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HLA-K	ENST00000430151.2	n.1000-283A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.465 AC: 67691 AN: 145426 Hom.: 19624 Cov.: 29

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.704

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.425

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.465 AC: 67719 AN: 145534 Hom.: 19628 Cov.: 29 AF XY: 0.467 AC XY: 33100 AN XY: 70916

Gnomad4 AFR AF: 0.464

Gnomad4 AMR AF: 0.500

Gnomad4 ASJ AF: 0.355

Gnomad4 EAS AF: 0.703

Gnomad4 SAS AF: 0.458

Gnomad4 FIN AF: 0.472

Gnomad4 NFE AF: 0.447

Gnomad4 OTH AF: 0.449

Alfa AF: 0.352 Hom.: 1686

Asia WGS AF: 0.582 AC: 1811 AN: 3114

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2517754; hg19: chr6-29896680;