rs913678

Variant names:

• chr20-50338887-T-C
• rs913678

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;