rs2571391

Variant names:

• chr6-29956061-A-C
• rs2571391
• ENST00000849680.1:n.1195T>G

Your query was ambiguous. Multiple possible variants found:

• chr6-29956061-A-C
• chr6-29956061-A-T

Variant summary

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

The ENST00000849680.1(POLR1HASP):​n.1195T>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 0.314 in 150,646 control chromosomes in the GnomAD database, including 6,883 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 0.31 (6883 hom., cov: 33)
• Consequence: POLR1HASP ENST00000849680.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.297
• Publications: 30 publications found

Genes affected

POLR1HASP (HGNC:):

HLA-W (HGNC:23425): (major histocompatibility complex, class I, W (pseudogene))

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HLA-W		n.29956061A>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POLR1HASP	ENST00000849680.1	n.1195T>G		non_coding_transcript_exon_variant	Exon 5 of 5
POLR1HASP	ENST00000849720.1	n.1345T>G		non_coding_transcript_exon_variant	Exon 2 of 2
POLR1HASP	ENST00000849721.1	n.987T>G		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47293 AN: 150534 Hom.: 6882 Cov.: 33

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.314 AC: 47308 AN: 150646 Hom.: 6883 Cov.: 33 AF XY: 0.313 AC XY: 23024 AN XY: 73636

African (AFR) AF: 0.269 AC: 11003 AN: 40924

American (AMR) AF: 0.336 AC: 5039 AN: 14980

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 862 AN: 3436

East Asian (EAS) AF: 0.290 AC: 1501 AN: 5174

South Asian (SAS) AF: 0.218 AC: 1047 AN: 4806

European-Finnish (FIN) AF: 0.387 AC: 4070 AN: 10514

Middle Eastern (MID) AF: 0.276 AC: 80 AN: 290

European-Non Finnish (NFE) AF: 0.337 AC: 22770 AN: 67536

Other (OTH) AF: 0.292 AC: 608 AN: 2080

Alfa AF: 0.332 Hom.: 3436

Asia WGS AF: 0.224 AC: 780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.67
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs2571391; hg19: chr6-29923838;