rs35476703

chr20-45174234-C-G

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 0.153 in 152,134 control chromosomes in the GnomAD database, including 1,908 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 (1908 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.172 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: 0.153 AC: 23209 AN: 152016 Hom.: 1903 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.0345

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.153 AC: 23248 AN: 152134 Hom.: 1908 Cov.: 32 AF XY: 0.154 AC XY: 11436 AN XY: 74382

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.0345

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.174

Gnomad4 OTH AF: 0.167

Alfa AF: 0.165 Hom.: 257

Bravo AF: 0.146

Asia WGS AF: 0.0930 AC: 323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.4
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35476703; hg19: chr20-43802875;