rs1934954

chr10-95032445-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 0.0554 in 152,248 control chromosomes in the GnomAD database, including 303 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 0.055 (303 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

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 = 0.078 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: 0.0554 AC: 8432 AN: 152130 Hom.: 303 Cov.: 33

Gnomad AFR AF: 0.0160

Gnomad AMI AF: 0.0319

Gnomad AMR AF: 0.0742

Gnomad ASJ AF: 0.0611

Gnomad EAS AF: 0.000576

Gnomad SAS AF: 0.0261

Gnomad FIN AF: 0.0625

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0797

Gnomad OTH AF: 0.0722

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

GnomAD4 genome AF: 0.0554 AC: 8429 AN: 152248 Hom.: 303 Cov.: 33 AF XY: 0.0537 AC XY: 3995 AN XY: 74436

Gnomad4 AFR AF: 0.0160

Gnomad4 AMR AF: 0.0741

Gnomad4 ASJ AF: 0.0611

Gnomad4 EAS AF: 0.000385

Gnomad4 SAS AF: 0.0262

Gnomad4 FIN AF: 0.0625

Gnomad4 NFE AF: 0.0797

Gnomad4 OTH AF: 0.0715

Alfa AF: 0.0686 Hom.: 107

Bravo AF: 0.0556

Asia WGS AF: 0.0110 AC: 40 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	4.0
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1934954; hg19: chr10-96792202;