ENST00000647952.1:n.2063-8038G>T

Variant names:

• chr6-29865476-C-A
• rs2734975
• ENST00000647952.1:n.2063-8038G>T

Variant summary

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

The ENST00000647952.1(ENSG00000290870):​n.2063-8038G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.482 in 152,042 control chromosomes in the GnomAD database, including 17,742 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 0.48 (17742 hom., cov: 33)
• Consequence: ENSG00000290870 ENST00000647952.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.878
• Publications: 10 publications found

Genes affected

ENSG00000290870 (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 (AMR) allele frequency at 95% confidence interval = 0.506 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
ENSG00000290870	ENST00000647952.1	n.2063-8038G>T		intron_variant	Intron 1 of 3
POLR1HASP	ENST00000849679.1	n.587-2650G>T		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73192 AN: 151924 Hom.: 17715 Cov.: 33

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.482 AC: 73256 AN: 152042 Hom.: 17742 Cov.: 33 AF XY: 0.480 AC XY: 35641 AN XY: 74302

African (AFR) AF: 0.512 AC: 21227 AN: 41468

American (AMR) AF: 0.512 AC: 7818 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.496 AC: 1721 AN: 3468

East Asian (EAS) AF: 0.435 AC: 2250 AN: 5172

South Asian (SAS) AF: 0.327 AC: 1574 AN: 4814

European-Finnish (FIN) AF: 0.465 AC: 4914 AN: 10558

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.474 AC: 32203 AN: 67974

Other (OTH) AF: 0.474 AC: 1002 AN: 2112

Alfa AF: 0.487 Hom.: 3317

Bravo AF: 0.493

Asia WGS AF: 0.320 AC: 1115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.35
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs2734975; hg19: chr6-29833253;