9-35141708-A-G

Variant names:

• chr9-35141708-A-G
• rs10972341

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 20 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.639 AC: 26452 AN: 41414

American (AMR) AF: 0.650 AC: 9927 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.648 AC: 2248 AN: 3468

East Asian (EAS) AF: 0.235 AC: 1215 AN: 5162

South Asian (SAS) AF: 0.358 AC: 1722 AN: 4810

European-Finnish (FIN) AF: 0.659 AC: 6965 AN: 10566

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.626 AC: 42550 AN: 67974

Other (OTH) AF: 0.607 AC: 1283 AN: 2112

Alfa AF: 0.617 Hom.: 83435

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
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs10972341; hg19: chr9-35141705;