20-37248607-T-C

Position:

• chr20-37248607-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 0.636 in 151,988 control chromosomes in the GnomAD database, including 33,372 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 0.64 (33372 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.320

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.907 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: 0.636 AC: 96631 AN: 151870 Hom.: 33323 Cov.: 30

Gnomad AFR AF: 0.915

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.636 AC: 96726 AN: 151988 Hom.: 33372 Cov.: 30 AF XY: 0.627 AC XY: 46580 AN XY: 74276

Gnomad4 AFR AF: 0.915

Gnomad4 AMR AF: 0.433

Gnomad4 ASJ AF: 0.579

Gnomad4 EAS AF: 0.375

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.537

Gnomad4 NFE AF: 0.571

Gnomad4 OTH AF: 0.594

Alfa AF: 0.561 Hom.: 32338

Bravo AF: 0.641

Asia WGS AF: 0.442 AC: 1541 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1073768; hg19: chr20-35877010;