rs7905355

chr10-124236026-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 0.336 in 152,008 control chromosomes in the GnomAD database, including 9,003 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 (9003 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.551

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.587 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: 0.336 AC: 51076 AN: 151890 Hom.: 8996 Cov.: 32

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.336 AC: 51121 AN: 152008 Hom.: 9003 Cov.: 32 AF XY: 0.340 AC XY: 25274 AN XY: 74290

Gnomad4 AFR AF: 0.269

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.342

Gnomad4 EAS AF: 0.604

Gnomad4 SAS AF: 0.336

Gnomad4 FIN AF: 0.382

Gnomad4 NFE AF: 0.346

Gnomad4 OTH AF: 0.330

Alfa AF: 0.348 Hom.: 19597

Bravo AF: 0.332

Asia WGS AF: 0.498 AC: 1727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.5
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7905355; hg19: chr10-125924595;