rs913678

Positions:

• chr20-50338887-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.507 in 152,172 control chromosomes in the GnomAD database, including 23,656 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 0.51 (23656 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.851 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.507 AC: 77066 AN: 152054 Hom.: 23597 Cov.: 33

Gnomad AFR AF: 0.859

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.507 AC: 77187 AN: 152172 Hom.: 23656 Cov.: 33 AF XY: 0.508 AC XY: 37777 AN XY: 74376

Gnomad4 AFR AF: 0.859

Gnomad4 AMR AF: 0.499

Gnomad4 ASJ AF: 0.422

Gnomad4 EAS AF: 0.675

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.360

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.514

Alfa AF: 0.366 Hom.: 7472

Bravo AF: 0.540

Asia WGS AF: 0.542 AC: 1884 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	17
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs913678; hg19: chr20-48955424;