rs10941694

Variant names:

• chr5-45197677-G-A
• rs10941694

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 0.145 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
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0569 AC: 2354 AN: 41384

American (AMR) AF: 0.228 AC: 3483 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 953 AN: 3470

East Asian (EAS) AF: 0.114 AC: 587 AN: 5160

South Asian (SAS) AF: 0.196 AC: 945 AN: 4812

European-Finnish (FIN) AF: 0.137 AC: 1438 AN: 10530

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.174 AC: 11801 AN: 67934

Other (OTH) AF: 0.158 AC: 333 AN: 2112

Alfa AF: 0.166 Hom.: 4606

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
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs10941694; hg19: chr5-45197779;