rs10274759

chr7-115274554-A-G

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 0.0385 in 152,282 control chromosomes in the GnomAD database, including 159 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 0.038 (159 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.275

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0687 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0384 AC: 5846 AN: 152164 Hom.: 157 Cov.: 32

Gnomad AFR AF: 0.0695

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0412

Gnomad ASJ AF: 0.0631

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0744

Gnomad FIN AF: 0.00621

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0230

Gnomad OTH AF: 0.0489

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

GnomAD4 genome AF: 0.0385 AC: 5861 AN: 152282 Hom.: 159 Cov.: 32 AF XY: 0.0376 AC XY: 2799 AN XY: 74456

Gnomad4 AFR AF: 0.0697

Gnomad4 AMR AF: 0.0411

Gnomad4 ASJ AF: 0.0631

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0751

Gnomad4 FIN AF: 0.00621

Gnomad4 NFE AF: 0.0230

Gnomad4 OTH AF: 0.0479

Alfa AF: 0.0312 Hom.: 18

Bravo AF: 0.0418

Asia WGS AF: 0.0400 AC: 140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
Cadd	Benign	13
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10274759; hg19: chr7-114914608;