rs718630

chr20-50494719-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 0.425 in 152,130 control chromosomes in the GnomAD database, including 13,775 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 0.43 (13775 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.452 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: 0.425 AC: 64655 AN: 152010 Hom.: 13768 Cov.: 33

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.425 AC: 64688 AN: 152130 Hom.: 13775 Cov.: 33 AF XY: 0.427 AC XY: 31745 AN XY: 74344

Gnomad4 AFR AF: 0.457

Gnomad4 AMR AF: 0.435

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.362

Gnomad4 SAS AF: 0.417

Gnomad4 FIN AF: 0.457

Gnomad4 NFE AF: 0.406

Gnomad4 OTH AF: 0.402

Alfa AF: 0.410 Hom.: 17036

Bravo AF: 0.422

Asia WGS AF: 0.421 AC: 1465 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.26
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs718630; hg19: chr20-49111256;