rs10969139

chr9-29412340-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;