ENST00000647952.1:n.2062+1712C>A

Variant names:

• chr6-29881842-G-T
• rs2523809
• ENST00000647952.1:n.2062+1712C>A

Variant summary

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

The ENST00000647952.1(ENSG00000290870):​n.2062+1712C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,292 control chromosomes in the GnomAD database, including 1,000 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 0.11 (1000 hom., cov: 34)
• Consequence: ENSG00000290870 ENST00000647952.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.313
• Publications: 48 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.128 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290870	ENST00000647952.1		n.2062+1712C>A		intron	N/A
	POLR1HASP	ENST00000849679.1		n.586+4444C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16555 AN: 152172 Hom.: 994 Cov.: 34

Gnomad AFR AF: 0.0790

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.0559

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.0759

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.109 AC: 16596 AN: 152292 Hom.: 1000 Cov.: 34 AF XY: 0.108 AC XY: 8079 AN XY: 74472

African (AFR) AF: 0.0796 AC: 3308 AN: 41566

American (AMR) AF: 0.132 AC: 2026 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 871 AN: 3468

East Asian (EAS) AF: 0.0561 AC: 291 AN: 5190

South Asian (SAS) AF: 0.106 AC: 509 AN: 4822

European-Finnish (FIN) AF: 0.0759 AC: 806 AN: 10624

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8371 AN: 68002

Other (OTH) AF: 0.130 AC: 275 AN: 2114

Alfa AF: 0.120 Hom.: 4746

Bravo AF: 0.111

Asia WGS AF: 0.0740 AC: 259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.3
DANN	Benign	0.28
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs2523809; hg19: chr6-29849619;