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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000849679.1. 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	ENST00000849679.1		n.66-3354C>T		intron	N/A
	POLR1HASP	ENST00000849682.1		n.751-3354C>T		intron	N/A
	POLR1HASP	ENST00000849693.1		n.1099+12881C>T		intron	N/A

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 v4.9

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

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

Other links and lift over

dbSNP: rs2524005;

hg19: chr6-29899677;