rs2571400

Variant names:

• chr6-29959945-C-G
• rs2571400
• ENST00000849678.1:n.589-13029G>C

Variant summary

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

The ENST00000849678.1(POLR1HASP):​n.589-13029G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 145,716 control chromosomes in the GnomAD database, including 18,372 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 0.51 (18372 hom., cov: 32)
• Consequence: POLR1HASP ENST00000849678.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.902
• Publications: 21 publications found

Genes affected

POLR1HASP (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.591 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
POLR1HASP	ENST00000849678.1	n.589-13029G>C		intron_variant	Intron 3 of 4
POLR1HASP	ENST00000849679.1	n.65+16658G>C		intron_variant	Intron 1 of 5
POLR1HASP	ENST00000849680.1	n.506-3195G>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.511 AC: 74382 AN: 145612 Hom.: 18354 Cov.: 32

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.511 AC: 74440 AN: 145716 Hom.: 18372 Cov.: 32 AF XY: 0.512 AC XY: 36498 AN XY: 71234

African (AFR) AF: 0.532 AC: 20404 AN: 38364

American (AMR) AF: 0.522 AC: 7617 AN: 14598

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1652 AN: 3350

East Asian (EAS) AF: 0.549 AC: 2652 AN: 4830

South Asian (SAS) AF: 0.610 AC: 2774 AN: 4550

European-Finnish (FIN) AF: 0.484 AC: 5042 AN: 10414

Middle Eastern (MID) AF: 0.550 AC: 153 AN: 278

European-Non Finnish (NFE) AF: 0.490 AC: 32524 AN: 66408

Other (OTH) AF: 0.520 AC: 1050 AN: 2018

Alfa AF: 0.484 Hom.: 9746

Asia WGS AF: 0.588 AC: 2030 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.2
DANN	Benign	0.18
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs2571400; hg19: chr6-29927722;