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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000849680.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POLR1HASP	ENST00000849680.1		n.1195T>G		non_coding_transcript_exon	Exon 5 of 5
	POLR1HASP	ENST00000849720.1		n.1345T>G		non_coding_transcript_exon	Exon 2 of 2
	POLR1HASP	ENST00000849721.1		n.987T>G		non_coding_transcript_exon	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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2571391;

hg19: chr6-29923838;