rs35476703

Variant names:

• chr20-45174234-C-G
• rs35476703

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 0.153 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
• Publications: 3 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.123 AC: 5088 AN: 41502

American (AMR) AF: 0.130 AC: 1987 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 725 AN: 3470

East Asian (EAS) AF: 0.0345 AC: 179 AN: 5182

South Asian (SAS) AF: 0.146 AC: 703 AN: 4824

European-Finnish (FIN) AF: 0.191 AC: 2017 AN: 10580

Middle Eastern (MID) AF: 0.240 AC: 70 AN: 292

European-Non Finnish (NFE) AF: 0.174 AC: 11842 AN: 67972

Other (OTH) AF: 0.167 AC: 353 AN: 2112

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
PhyloP100		0.024

Splicing

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

Other links and lift over

dbSNP: rs35476703; hg19: chr20-43802875;