rs718630

Variant names:

• chr20-50494719-T-G
• rs718630

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.457 AC: 18976 AN: 41514

American (AMR) AF: 0.435 AC: 6651 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1501 AN: 3470

East Asian (EAS) AF: 0.362 AC: 1870 AN: 5170

South Asian (SAS) AF: 0.417 AC: 2014 AN: 4830

European-Finnish (FIN) AF: 0.457 AC: 4820 AN: 10558

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.406 AC: 27630 AN: 67990

Other (OTH) AF: 0.402 AC: 850 AN: 2112

Alfa AF: 0.411 Hom.: 21638

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs718630; hg19: chr20-49111256;