rs10950426

Positions:

• chr7-12893424-G-A

Variant summary

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

The ENST00000639998.1(ENSG00000229618):​n.483+135108G>A variant causes a intron, non coding transcript 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: ENST00000639998.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.102

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000639998.1	n.483+135108G>A		intron_variant, non_coding_transcript_variant		5
	ENST00000638964.1	n.484+90692G>A		intron_variant, non_coding_transcript_variant		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;