rs10950426

Variant names:

• chr7-12893424-G-A
• rs10950426
• ENST00000638964.1:n.484+90692G>A

Variant summary

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

The ENST00000638964.1(ENSG00000229618):​n.484+90692G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 151,794 control chromosomes in the GnomAD database, including 7,071 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 0.29 (7071 hom., cov: 32)
• Consequence: ENSG00000229618 ENST00000638964.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.102

Genes affected

ENSG00000229618 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.358 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
ENSG00000229618	ENST00000638964.1	n.484+90692G>A		intron_variant	Intron 1 of 5	5
ENSG00000229618	ENST00000639998.1	n.483+135108G>A		intron_variant	Intron 3 of 7	5

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44413 AN: 151678 Hom.: 7063 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.293 AC: 44438 AN: 151794 Hom.: 7071 Cov.: 32 AF XY: 0.291 AC XY: 21582 AN XY: 74168

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.338

Gnomad4 EAS AF: 0.310

Gnomad4 SAS AF: 0.368

Gnomad4 FIN AF: 0.272

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.313

Alfa AF: 0.341 Hom.: 11919

Bravo AF: 0.293

Asia WGS AF: 0.297 AC: 1035 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	2.0
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10950426; hg19: chr7-12933049;