rs10969139

Variant names:

• chr9-29412340-T-C
• rs10969139

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 0.0351 in 151,000 control chromosomes in the GnomAD database, including 123 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 0.035 (123 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.97

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0821 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: 0.0351 AC: 5297 AN: 150882 Hom.: 123 Cov.: 32

Gnomad AFR AF: 0.0350

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.0303

Gnomad ASJ AF: 0.0250

Gnomad EAS AF: 0.0890

Gnomad SAS AF: 0.0263

Gnomad FIN AF: 0.0219

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0340

Gnomad OTH AF: 0.0300

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

GnomAD4 genome AF: 0.0351 AC: 5301 AN: 151000 Hom.: 123 Cov.: 32 AF XY: 0.0343 AC XY: 2533 AN XY: 73758

Gnomad4 AFR AF: 0.0350

Gnomad4 AMR AF: 0.0304

Gnomad4 ASJ AF: 0.0250

Gnomad4 EAS AF: 0.0888

Gnomad4 SAS AF: 0.0268

Gnomad4 FIN AF: 0.0219

Gnomad4 NFE AF: 0.0340

Gnomad4 OTH AF: 0.0297

Alfa AF: 0.0342 Hom.: 21

Bravo AF: 0.0381

Asia WGS AF: 0.0440 AC: 153 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.015
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10969139; hg19: chr9-29412338; COSMIC: COSV69456967;