rs10972341

Positions:

• chr9-35141708-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 0.612 in 151,990 control chromosomes in the GnomAD database, including 29,075 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 0.61 (29075 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.960

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.639 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: 0.612 AC: 92945 AN: 151872 Hom.: 29035 Cov.: 31

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.612 AC: 93041 AN: 151990 Hom.: 29075 Cov.: 31 AF XY: 0.605 AC XY: 44955 AN XY: 74280

Gnomad4 AFR AF: 0.639

Gnomad4 AMR AF: 0.650

Gnomad4 ASJ AF: 0.648

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.659

Gnomad4 NFE AF: 0.626

Gnomad4 OTH AF: 0.607

Alfa AF: 0.617 Hom.: 55359

Bravo AF: 0.614

Asia WGS AF: 0.338 AC: 1179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.9
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10972341; hg19: chr9-35141705;