rs10953089

Positions:

• chr7-93099114-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 0.32 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.546

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.529

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.195

Gnomad4 OTH AF: 0.323

Alfa AF: 0.221 Hom.: 5730

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

Splicing

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

Publications

LitVar

Other links and lift over

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