20-49496763-T-C

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 0.149 in 152,144 control chromosomes in the GnomAD database, including 1,737 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 (1737 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.185 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: 0.149 AC: 22608 AN: 152026 Hom.: 1740 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.149 AC: 22595 AN: 152144 Hom.: 1737 Cov.: 32 AF XY: 0.147 AC XY: 10962 AN XY: 74386

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.192

Alfa AF: 0.173 Hom.: 2080

Bravo AF: 0.150

Asia WGS AF: 0.163 AC: 566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
Cadd	Benign	9.4
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6095543; hg19: chr20-48113300;