rs10248926

Positions:

• chr7-70892343-G-A
• chr7-70892343-G-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 0.398 in 151,744 control chromosomes in the GnomAD database, including 13,101 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 0.40 (13101 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.23

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.488 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: 0.398 AC: 60368 AN: 151626 Hom.: 13095 Cov.: 31

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.398 AC: 60390 AN: 151744 Hom.: 13101 Cov.: 31 AF XY: 0.405 AC XY: 30024 AN XY: 74114

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.505

Gnomad4 SAS AF: 0.427

Gnomad4 FIN AF: 0.613

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.404

Alfa AF: 0.431 Hom.: 2938

Bravo AF: 0.382

Asia WGS AF: 0.411 AC: 1430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.57
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10248926; hg19: chr7-70357329;