6-29817999-C-T

Variant names:

• chr6-29817999-C-T
• rs1736951
• ENST00000849927.1:n.26+10472G>A

Variant summary

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

The ENST00000849927.1(HLA-F-AS1):​n.26+10472G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 152,040 control chromosomes in the GnomAD database, including 9,141 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 0.34 (9141 hom., cov: 31)
• Consequence: HLA-F-AS1 ENST00000849927.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.586
• Publications: 16 publications found

Genes affected

HLA-F-AS1 (HGNC:26645): (HLA-F antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HLA-F-AS1	ENST00000849927.1	n.26+10472G>A		intron_variant	Intron 1 of 3
HLA-F-AS1	ENST00000849935.1	n.230+9721G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51975 AN: 151920 Hom.: 9128 Cov.: 31

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.342 AC: 52026 AN: 152040 Hom.: 9141 Cov.: 31 AF XY: 0.335 AC XY: 24869 AN XY: 74322

African (AFR) AF: 0.373 AC: 15463 AN: 41448

American (AMR) AF: 0.375 AC: 5727 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1658 AN: 3472

East Asian (EAS) AF: 0.121 AC: 628 AN: 5174

South Asian (SAS) AF: 0.325 AC: 1565 AN: 4816

European-Finnish (FIN) AF: 0.223 AC: 2362 AN: 10586

Middle Eastern (MID) AF: 0.466 AC: 136 AN: 292

European-Non Finnish (NFE) AF: 0.346 AC: 23494 AN: 67944

Other (OTH) AF: 0.358 AC: 755 AN: 2110

Alfa AF: 0.351 Hom.: 18017

Bravo AF: 0.357

Asia WGS AF: 0.215 AC: 751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.3
DANN	Benign	0.34
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs1736951; hg19: chr6-29785776;