ENST00000647952.1:n.2063-3665G>A

Variant names:

• chr6-29861103-C-T
• rs9295822
• ENST00000647952.1:n.2063-3665G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000647952.1(ENSG00000290870):​n.2063-3665G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 152,166 control chromosomes in the GnomAD database, including 1,424 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 (1424 hom., cov: 31)
• Consequence: ENSG00000290870 ENST00000647952.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

Genes affected

ENSG00000290870 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.235 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.2063-3665G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.112 AC: 16994 AN: 152048 Hom.: 1422 Cov.: 31

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.0749

Gnomad EAS AF: 0.0245

Gnomad SAS AF: 0.0676

Gnomad FIN AF: 0.0525

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0535

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.112 AC: 17011 AN: 152166 Hom.: 1424 Cov.: 31 AF XY: 0.111 AC XY: 8280 AN XY: 74412

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.0749

Gnomad4 EAS AF: 0.0245

Gnomad4 SAS AF: 0.0674

Gnomad4 FIN AF: 0.0525

Gnomad4 NFE AF: 0.0535

Gnomad4 OTH AF: 0.111

Alfa AF: 0.0761 Hom.: 361

Bravo AF: 0.126

Asia WGS AF: 0.0510 AC: 177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.9
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9295822; hg19: chr6-29828880;