rs3810458

chr20-62707832-T-Cchr20-62707832-T-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 0.255 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.220

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.0483

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.242

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.250

Alfa AF: 0.250 Hom.: 4675

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3810458; hg19: chr20-61339184;