rs10953089

Variant names:

• chr7-93099114-C-T
• rs10953089

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 0.32 in 151,996 control chromosomes in the GnomAD database, including 9,869 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 0.32 (9869 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.54 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: 0.320 AC: 48541 AN: 151878 Hom.: 9838 Cov.: 32

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.320 AC: 48627 AN: 151996 Hom.: 9869 Cov.: 32 AF XY: 0.316 AC XY: 23444 AN XY: 74302

African (AFR) AF: 0.546 AC: 22616 AN: 41402

American (AMR) AF: 0.407 AC: 6207 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 910 AN: 3466

East Asian (EAS) AF: 0.529 AC: 2737 AN: 5172

South Asian (SAS) AF: 0.131 AC: 634 AN: 4822

European-Finnish (FIN) AF: 0.134 AC: 1418 AN: 10576

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.195 AC: 13221 AN: 67974

Other (OTH) AF: 0.323 AC: 683 AN: 2114

Alfa AF: 0.235 Hom.: 8426

Bravo AF: 0.356

Asia WGS AF: 0.352 AC: 1224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.9
DANN	Benign	0.27
PhyloP100		-0.047

Splicing

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

Other links and lift over

dbSNP: rs10953089; hg19: chr7-92728427; COSMIC: COSV66073544;