rs10952296

Positions:

• chr7-150987742-C-A
• chr7-150987742-C-T

Variant summary

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

The variant allele was found at a frequency of 0.336 in 151,732 control chromosomes in the GnomAD database, including 9,706 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 0.34 (9706 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.623

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.731 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

Frequencies

GnomAD3 genomes AF: 0.336 AC: 50976 AN: 151614 Hom.: 9676 Cov.: 30

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.336 AC: 51050 AN: 151732 Hom.: 9706 Cov.: 30 AF XY: 0.345 AC XY: 25555 AN XY: 74140

Gnomad4 AFR AF: 0.438

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.313

Gnomad4 EAS AF: 0.750

Gnomad4 SAS AF: 0.452

Gnomad4 FIN AF: 0.300

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.324

Alfa AF: 0.281 Hom.: 1706

Bravo AF: 0.350

Asia WGS AF: 0.588 AC: 2039 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.8
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10952296; hg19: chr7-150684830;