rs535964

Variant names:

• chr20-3685839-G-A
• rs535964

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 0.393 in 152,042 control chromosomes in the GnomAD database, including 11,738 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 0.39 (11738 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.424 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: 0.393 AC: 59725 AN: 151924 Hom.: 11722 Cov.: 33

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.393 AC: 59778 AN: 152042 Hom.: 11738 Cov.: 33 AF XY: 0.389 AC XY: 28907 AN XY: 74324

African (AFR) AF: 0.429 AC: 17800 AN: 41466

American (AMR) AF: 0.369 AC: 5639 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1155 AN: 3472

East Asian (EAS) AF: 0.269 AC: 1389 AN: 5170

South Asian (SAS) AF: 0.348 AC: 1678 AN: 4816

European-Finnish (FIN) AF: 0.379 AC: 4012 AN: 10576

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.394 AC: 26799 AN: 67952

Other (OTH) AF: 0.372 AC: 785 AN: 2112

Alfa AF: 0.393 Hom.: 1476

Bravo AF: 0.392

Asia WGS AF: 0.379 AC: 1315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.7
DANN	Benign	0.42
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs535964; hg19: chr20-3666486;