9-96175380-T-C

Variant names:

• chr9-96175380-T-C
• rs10512241

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 0.661 in 152,120 control chromosomes in the GnomAD database, including 33,437 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 0.66 (33437 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.762 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: 0.661 AC: 100416 AN: 152002 Hom.: 33405 Cov.: 33

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.785

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.759

Gnomad EAS AF: 0.783

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.661 AC: 100501 AN: 152120 Hom.: 33437 Cov.: 33 AF XY: 0.656 AC XY: 48788 AN XY: 74376

African (AFR) AF: 0.695 AC: 28811 AN: 41474

American (AMR) AF: 0.639 AC: 9776 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.759 AC: 2633 AN: 3470

East Asian (EAS) AF: 0.782 AC: 4055 AN: 5184

South Asian (SAS) AF: 0.640 AC: 3085 AN: 4822

European-Finnish (FIN) AF: 0.514 AC: 5433 AN: 10568

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.652 AC: 44309 AN: 67990

Other (OTH) AF: 0.684 AC: 1445 AN: 2114

Alfa AF: 0.648 Hom.: 20962

Bravo AF: 0.673

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.23
DANN	Benign	0.42
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs10512241; hg19: chr9-98937662;