rs953183

chr7-106968592-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 0.427 in 152,006 control chromosomes in the GnomAD database, including 14,282 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 0.43 (14282 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.48

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.473 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: 0.427 AC: 64848 AN: 151888 Hom.: 14279 Cov.: 32

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.427 AC: 64869 AN: 152006 Hom.: 14282 Cov.: 32 AF XY: 0.426 AC XY: 31648 AN XY: 74280

Gnomad4 AFR AF: 0.342

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.426

Gnomad4 EAS AF: 0.449

Gnomad4 SAS AF: 0.427

Gnomad4 FIN AF: 0.496

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.433

Alfa AF: 0.461 Hom.: 3386

Bravo AF: 0.414

Asia WGS AF: 0.421 AC: 1466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	8.3
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs953183; hg19: chr7-106609037;