20-49962811-G-T

Variant names:

• chr20-49962811-G-T
• rs4810997

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 0.389 in 151,910 control chromosomes in the GnomAD database, including 13,200 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 (13200 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.819

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.674 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: 0.389 AC: 59010 AN: 151792 Hom.: 13187 Cov.: 31

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.693

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.389 AC: 59057 AN: 151910 Hom.: 13200 Cov.: 31 AF XY: 0.405 AC XY: 30032 AN XY: 74210

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.508

Gnomad4 ASJ AF: 0.331

Gnomad4 EAS AF: 0.693

Gnomad4 SAS AF: 0.597

Gnomad4 FIN AF: 0.585

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.384

Alfa AF: 0.403 Hom.: 16261

Bravo AF: 0.369

Asia WGS AF: 0.609 AC: 2118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.58
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4810997; hg19: chr20-48579348;