rs1611213

Variant names:

• chr6-29792813-G-A
• rs1611213
• ENST00000446817.1:n.559G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-29792813-G-A
• chr6-29792813-G-C
• chr6-29792813-G-T

Variant summary

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

The ENST00000446817.1(HLA-V):​n.559G>A 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 0.34 in 1,040,490 control chromosomes in the GnomAD database, including 62,705 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 0.39 (12368 hom., cov: 31)
  • Exomes 𝑓: 0.33 (50337 hom.)
• Consequence: HLA-V ENST00000446817.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.349
• Publications: 9 publications found

Genes affected

HLA-V (HGNC:):

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

HCG4 (HGNC:21241): (HLA complex group 4)

HLA-V (HGNC:23482): (major histocompatibility complex, class I, V (pseudogene))

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HCG4	NR_002139.2	n.261C>T		non_coding_transcript_exon_variant	Exon 1 of 1
HLA-V	NR_132323.1	n.670+107G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HLA-V	ENST00000446817.1	n.559G>A		non_coding_transcript_exon_variant	Exon 4 of 4	6
HLA-F-AS1	ENST00000849876.1	n.89C>T		non_coding_transcript_exon_variant	Exon 1 of 2
HLA-F-AS1	ENST00000849921.1	n.109C>T		non_coding_transcript_exon_variant	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.389 AC: 59058 AN: 151684 Hom.: 12353 Cov.: 31

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.402

GnomAD4 exome AF: 0.332 AC: 294974 AN: 888688 Hom.: 50337 Cov.: 12 AF XY: 0.334 AC XY: 143026 AN XY: 428744

African (AFR) AF: 0.525 AC: 8748 AN: 16654

American (AMR) AF: 0.299 AC: 3017 AN: 10092

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 3485 AN: 8182

East Asian (EAS) AF: 0.159 AC: 1715 AN: 10806

South Asian (SAS) AF: 0.371 AC: 20061 AN: 54032

European-Finnish (FIN) AF: 0.208 AC: 2430 AN: 11706

Middle Eastern (MID) AF: 0.393 AC: 1285 AN: 3272

European-Non Finnish (NFE) AF: 0.328 AC: 243465 AN: 741700

Other (OTH) AF: 0.334 AC: 10768 AN: 32244

GnomAD4 genome AF: 0.389 AC: 59107 AN: 151802 Hom.: 12368 Cov.: 31 AF XY: 0.381 AC XY: 28253 AN XY: 74194

African (AFR) AF: 0.543 AC: 22471 AN: 41356

American (AMR) AF: 0.385 AC: 5889 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1589 AN: 3464

East Asian (EAS) AF: 0.199 AC: 1020 AN: 5116

South Asian (SAS) AF: 0.353 AC: 1699 AN: 4812

European-Finnish (FIN) AF: 0.206 AC: 2182 AN: 10570

Middle Eastern (MID) AF: 0.483 AC: 141 AN: 292

European-Non Finnish (NFE) AF: 0.340 AC: 23095 AN: 67896

Other (OTH) AF: 0.397 AC: 834 AN: 2102

Alfa AF: 0.373 Hom.: 3430

Bravo AF: 0.413

Asia WGS AF: 0.280 AC: 976 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	13
DANN	Benign	0.93
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs1611213; hg19: chr6-29760590; COSMIC: COSV57641536;