chr9-111102370-C-T

Variant names:

• chr9-111102370-C-T
• rs10491533

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 0.717 in 152,136 control chromosomes in the GnomAD database, including 40,259 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 0.72 (40259 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.893 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: 0.717 AC: 109024 AN: 152018 Hom.: 40194 Cov.: 32

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.732

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.720

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.707

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

GnomAD4 genome AF: 0.717 AC: 109144 AN: 152136 Hom.: 40259 Cov.: 32 AF XY: 0.720 AC XY: 53509 AN XY: 74364

African (AFR) AF: 0.901 AC: 37403 AN: 41528

American (AMR) AF: 0.678 AC: 10351 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.692 AC: 2399 AN: 3468

East Asian (EAS) AF: 0.731 AC: 3786 AN: 5180

South Asian (SAS) AF: 0.764 AC: 3683 AN: 4818

European-Finnish (FIN) AF: 0.660 AC: 6975 AN: 10574

Middle Eastern (MID) AF: 0.719 AC: 210 AN: 292

European-Non Finnish (NFE) AF: 0.620 AC: 42138 AN: 67976

Other (OTH) AF: 0.711 AC: 1503 AN: 2114

Alfa AF: 0.654 Hom.: 18166

Bravo AF: 0.724

Asia WGS AF: 0.782 AC: 2718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.12
DANN	Benign	0.69
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs10491533; hg19: chr9-113864650;