7-95443304-A-G

Variant names:

• chr7-95443304-A-G
• rs10953147
• ENST00000818771.1:n.639+7699A>G

Variant summary

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

The ENST00000818771.1(ENSG00000233942):​n.639+7699A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 151,772 control chromosomes in the GnomAD database, including 18,419 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 0.49 (18419 hom., cov: 31)
• Consequence: ENSG00000233942 ENST00000818771.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.460
• Publications: 6 publications found

Genes affected

ENSG00000233942 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.774 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
ENSG00000233942	ENST00000818771.1	n.639+7699A>G		intron_variant	Intron 2 of 8
ENSG00000233942	ENST00000818772.1	n.464-27388A>G		intron_variant	Intron 1 of 2
ENSG00000233942	ENST00000818773.1	n.553+7699A>G		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73816 AN: 151654 Hom.: 18407 Cov.: 31

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.794

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.487 AC: 73866 AN: 151772 Hom.: 18419 Cov.: 31 AF XY: 0.496 AC XY: 36729 AN XY: 74110

African (AFR) AF: 0.445 AC: 18409 AN: 41404

American (AMR) AF: 0.525 AC: 7998 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1478 AN: 3470

East Asian (EAS) AF: 0.794 AC: 4062 AN: 5116

South Asian (SAS) AF: 0.665 AC: 3209 AN: 4822

European-Finnish (FIN) AF: 0.561 AC: 5875 AN: 10466

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31249 AN: 67954

Other (OTH) AF: 0.468 AC: 986 AN: 2106

Alfa AF: 0.465 Hom.: 9694

Bravo AF: 0.480

Asia WGS AF: 0.699 AC: 2426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	14
DANN	Benign	0.92
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs10953147; hg19: chr7-95072616;