rs10901296

Variant names:

• chr9-130890269-G-A
• rs10901296

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 0.0465 in 152,238 control chromosomes in the GnomAD database, including 233 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 0.046 (233 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.825
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0694 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: 0.0466 AC: 7082 AN: 152120 Hom.: 233 Cov.: 32

Gnomad AFR AF: 0.0134

Gnomad AMI AF: 0.0549

Gnomad AMR AF: 0.0566

Gnomad ASJ AF: 0.0622

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0240

Gnomad FIN AF: 0.0281

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0711

Gnomad OTH AF: 0.0593

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

GnomAD4 genome AF: 0.0465 AC: 7079 AN: 152238 Hom.: 233 Cov.: 32 AF XY: 0.0433 AC XY: 3220 AN XY: 74446

African (AFR) AF: 0.0134 AC: 558 AN: 41540

American (AMR) AF: 0.0564 AC: 863 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0622 AC: 216 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5180

South Asian (SAS) AF: 0.0241 AC: 116 AN: 4822

European-Finnish (FIN) AF: 0.0281 AC: 298 AN: 10608

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0711 AC: 4833 AN: 68004

Other (OTH) AF: 0.0587 AC: 124 AN: 2114

Alfa AF: 0.0626 Hom.: 253

Bravo AF: 0.0459

Asia WGS AF: 0.0120 AC: 40 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	0.045
DANN	Benign	0.62
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs10901296; hg19: chr9-133765656;