rs1610640

Variant names:

• chr6-29790748-T-C
• rs1610640
• ENST00000849921.1:n.2174A>G

Variant summary

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

The ENST00000849921.1(HLA-F-AS1):​n.2174A>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 0.405 in 152,150 control chromosomes in the GnomAD database, including 13,506 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 0.41 (13506 hom., cov: 33)
• Consequence: HLA-F-AS1 ENST00000849921.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330
• Publications: 16 publications found

Genes affected

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

HLA-V (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.562 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	ENST00000849921.1	n.2174A>G		non_coding_transcript_exon_variant	Exon 1 of 1
HLA-F-AS1	ENST00000849873.1	n.421+1359A>G		intron_variant	Intron 1 of 1
HLA-F-AS1	ENST00000849874.1	n.403+1359A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61571 AN: 152032 Hom.: 13484 Cov.: 33

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.405 AC: 61631 AN: 152150 Hom.: 13506 Cov.: 33 AF XY: 0.396 AC XY: 29452 AN XY: 74376

African (AFR) AF: 0.568 AC: 23572 AN: 41468

American (AMR) AF: 0.415 AC: 6345 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1718 AN: 3472

East Asian (EAS) AF: 0.202 AC: 1046 AN: 5186

South Asian (SAS) AF: 0.356 AC: 1715 AN: 4820

European-Finnish (FIN) AF: 0.207 AC: 2188 AN: 10590

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.350 AC: 23812 AN: 68008

Other (OTH) AF: 0.424 AC: 895 AN: 2110

Alfa AF: 0.369 Hom.: 6412

Bravo AF: 0.431

Asia WGS AF: 0.288 AC: 1004 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.7
DANN	Benign	0.59
PhyloP100		0.033

Splicing

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

Other links and lift over

dbSNP: rs1610640; hg19: chr6-29758525;