rs10967991

Variant names:

• chr9-27574805-C-T
• rs10967991

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 0.184 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.117 AC: 4875 AN: 41522

American (AMR) AF: 0.141 AC: 2155 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 836 AN: 3468

East Asian (EAS) AF: 0.0949 AC: 491 AN: 5174

South Asian (SAS) AF: 0.188 AC: 905 AN: 4820

European-Finnish (FIN) AF: 0.232 AC: 2457 AN: 10580

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15736 AN: 67970

Other (OTH) AF: 0.177 AC: 375 AN: 2114

Alfa AF: 0.198 Hom.: 486

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
PhyloP100		-0.66

Splicing

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

Other links and lift over

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