rs10967991

chr9-27574805-C-T

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 0.184 in 152,142 control chromosomes in the GnomAD database, including 2,868 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 0.18 (2868 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.657

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.228 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: 0.184 AC: 27995 AN: 152024 Hom.: 2866 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.0951

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.184 AC: 28000 AN: 152142 Hom.: 2868 Cov.: 32 AF XY: 0.182 AC XY: 13556 AN XY: 74384

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.0949

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.177

Alfa AF: 0.201 Hom.: 480

Bravo AF: 0.170

Asia WGS AF: 0.168 AC: 583 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.2
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10967991; hg19: chr9-27574803; COSMIC: COSV66155089;