rs3810458

Variant names:

• chr20-62707832-T-C
• rs3810458

Your query was ambiguous. Multiple possible variants found:

• chr20-62707832-T-C
• chr20-62707832-T-G

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 0.255 in 152,048 control chromosomes in the GnomAD database, including 5,260 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 0.25 (5260 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.980
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.288 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: 0.255 AC: 38738 AN: 151930 Hom.: 5254 Cov.: 33

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.0484

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.255 AC: 38761 AN: 152048 Hom.: 5260 Cov.: 33 AF XY: 0.250 AC XY: 18588 AN XY: 74322

African (AFR) AF: 0.292 AC: 12114 AN: 41456

American (AMR) AF: 0.220 AC: 3363 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 805 AN: 3468

East Asian (EAS) AF: 0.0483 AC: 249 AN: 5158

South Asian (SAS) AF: 0.127 AC: 610 AN: 4816

European-Finnish (FIN) AF: 0.242 AC: 2560 AN: 10584

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18314 AN: 67950

Other (OTH) AF: 0.250 AC: 526 AN: 2106

Alfa AF: 0.253 Hom.: 5788

Bravo AF: 0.257

Asia WGS AF: 0.101 AC: 350 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.5
DANN	Benign	0.72
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs3810458; hg19: chr20-61339184;