20-37248607-T-C

Variant names:

• chr20-37248607-T-C
• rs1073768

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;