rs2524005

Variant names:

• chr6-29931900-G-A
• rs2524005
• ENST00000849679.1:n.66-3354C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-29931900-G-A
• chr6-29931900-G-C
• chr6-29931900-G-T

Variant summary

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

The ENST00000849679.1(POLR1HASP):​n.66-3354C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 146,910 control chromosomes in the GnomAD database, including 2,918 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 0.18 (2918 hom., cov: 27)
• Consequence: POLR1HASP ENST00000849679.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.227
• Publications: 59 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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901298	XR_007059541.1	n.814-3163C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POLR1HASP	ENST00000849679.1	n.66-3354C>T		intron_variant	Intron 1 of 5
POLR1HASP	ENST00000849682.1	n.751-3354C>T		intron_variant	Intron 1 of 3
POLR1HASP	ENST00000849693.1	n.1099+12881C>T		intron_variant	Intron 1 of 1
POLR1HASP	ENST00000849697.1	n.280-3354C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.180 AC: 26480 AN: 146796 Hom.: 2909 Cov.: 27

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.226

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.180 AC: 26504 AN: 146910 Hom.: 2918 Cov.: 27 AF XY: 0.177 AC XY: 12654 AN XY: 71664

African (AFR) AF: 0.161 AC: 6399 AN: 39860

American (AMR) AF: 0.151 AC: 2172 AN: 14408

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 618 AN: 3374

East Asian (EAS) AF: 0.143 AC: 680 AN: 4740

South Asian (SAS) AF: 0.282 AC: 1257 AN: 4456

European-Finnish (FIN) AF: 0.123 AC: 1277 AN: 10356

Middle Eastern (MID) AF: 0.223 AC: 62 AN: 278

European-Non Finnish (NFE) AF: 0.203 AC: 13524 AN: 66530

Other (OTH) AF: 0.175 AC: 352 AN: 2016

Alfa AF: 0.195 Hom.: 9934

Asia WGS AF: 0.189 AC: 658 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.1
DANN	Benign	0.12
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs2524005; hg19: chr6-29899677;