chr6-29928903-A-G

Variant names:

• chr6-29928903-A-G
• rs2517754
• ENST00000850461.1:n.56A>G

Variant summary

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

The ENST00000850461.1(ENSG00000310496):​n.56A>G 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 0.465 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: ENSG00000310496 ENST00000850461.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.529
• Publications: 14 publications found

Genes affected

ENSG00000310496 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
HLA-K		n.29928903A>G		intragenic_variant
LOC124901298	XR_007059541.1	n.814-166T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000310496	ENST00000850461.1	n.56A>G		non_coding_transcript_exon_variant	Exon 1 of 3
HLA-K	ENST00000430151.2	n.1000-283A>G		intron_variant	Intron 5 of 5	6
POLR1HASP	ENST00000849679.1	n.66-357T>C		intron_variant	Intron 1 of 5

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

African (AFR) AF: 0.464 AC: 18211 AN: 39270

American (AMR) AF: 0.500 AC: 7156 AN: 14306

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 1196 AN: 3366

East Asian (EAS) AF: 0.703 AC: 3262 AN: 4640

South Asian (SAS) AF: 0.458 AC: 2021 AN: 4414

European-Finnish (FIN) AF: 0.472 AC: 4798 AN: 10166

Middle Eastern (MID) AF: 0.420 AC: 115 AN: 274

European-Non Finnish (NFE) AF: 0.447 AC: 29627 AN: 66230

Other (OTH) AF: 0.449 AC: 888 AN: 1978

Alfa AF: 0.398 Hom.: 3466

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
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs2517754; hg19: chr6-29896680;