rs3903160

Variant names:

• chr6-29965120-G-A
• rs3903160
• ENST00000849678.1:n.589-18204C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-29965120-G-A
• chr6-29965120-G-C
• chr6-29965120-G-T

Variant summary

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

The ENST00000849678.1(POLR1HASP):​n.589-18204C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 144,618 control chromosomes in the GnomAD database, including 5,528 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 0.27 (5528 hom., cov: 32)
• Consequence: POLR1HASP ENST00000849678.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.814
• Publications: 29 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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000849678.1. 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	ENST00000849678.1		n.589-18204C>T		intron	N/A
	POLR1HASP	ENST00000849679.1		n.65+11483C>T		intron	N/A
	POLR1HASP	ENST00000849680.1		n.506-8370C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.274 AC: 39662 AN: 144524 Hom.: 5524 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.274 AC: 39675 AN: 144618 Hom.: 5528 Cov.: 32 AF XY: 0.275 AC XY: 19389 AN XY: 70536

African (AFR) AF: 0.217 AC: 8104 AN: 37390

American (AMR) AF: 0.283 AC: 4070 AN: 14406

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 635 AN: 3392

East Asian (EAS) AF: 0.312 AC: 1507 AN: 4826

South Asian (SAS) AF: 0.175 AC: 755 AN: 4306

European-Finnish (FIN) AF: 0.367 AC: 3817 AN: 10388

Middle Eastern (MID) AF: 0.228 AC: 63 AN: 276

European-Non Finnish (NFE) AF: 0.299 AC: 19951 AN: 66766

Other (OTH) AF: 0.256 AC: 505 AN: 1972

Alfa AF: 0.279 Hom.: 14060

Bravo AF: 0.255

Asia WGS AF: 0.197 AC: 679 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.7
DANN	Benign	0.71
PhyloP100		0.81

Splicing

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

Other links and lift over

dbSNP: rs3903160; hg19: chr6-29932897;