rs10941694

Positions:

• chr5-45197677-G-A

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 0.145 in 151,878 control chromosomes in the GnomAD database, including 1,939 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 0.15 (1939 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.384

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.222 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: 0.146 AC: 22094 AN: 151760 Hom.: 1943 Cov.: 32

Gnomad AFR AF: 0.0570

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.145 AC: 22087 AN: 151878 Hom.: 1939 Cov.: 32 AF XY: 0.148 AC XY: 10966 AN XY: 74222

Gnomad4 AFR AF: 0.0569

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.174

Gnomad4 OTH AF: 0.158

Alfa AF: 0.174 Hom.: 2810

Bravo AF: 0.149

Asia WGS AF: 0.152 AC: 524 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.44
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10941694; hg19: chr5-45197779;