rs1611635

Variant names:

• chr6-29868686-C-T
• rs1611635
• ENST00000647952.1:n.2063-11248G>A

Variant summary

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

The ENST00000647952.1(ENSG00000290870):​n.2063-11248G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,278 control chromosomes in the GnomAD database, including 1,108 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 0.10 (1108 hom., cov: 33)
• Consequence: ENSG00000290870 ENST00000647952.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 19 publications found

Genes affected

ENSG00000290870 (HGNC:59164):

POLR1HASP (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000647952.1. 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
	ENSG00000290870	ENST00000647952.1		n.2063-11248G>A		intron	N/A
	POLR1HASP	ENST00000849679.1		n.587-5860G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15789 AN: 152160 Hom.: 1108 Cov.: 33

Gnomad AFR AF: 0.0334

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.0675

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.0183

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.0781

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.0981

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

GnomAD4 genome AF: 0.104 AC: 15782 AN: 152278 Hom.: 1108 Cov.: 33 AF XY: 0.0988 AC XY: 7354 AN XY: 74460

African (AFR) AF: 0.0333 AC: 1385 AN: 41560

American (AMR) AF: 0.0674 AC: 1031 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 418 AN: 3464

East Asian (EAS) AF: 0.0183 AC: 95 AN: 5190

South Asian (SAS) AF: 0.128 AC: 616 AN: 4820

European-Finnish (FIN) AF: 0.0781 AC: 829 AN: 10610

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 11009 AN: 68018

Other (OTH) AF: 0.0975 AC: 206 AN: 2112

Alfa AF: 0.137 Hom.: 3154

Bravo AF: 0.0984

Asia WGS AF: 0.0630 AC: 222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.50
PhyloP100		-1.1

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: rs1611635;

hg19: chr6-29836463;