rs2748666

Positions:

• chr20-38777103-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 0.417 in 151,886 control chromosomes in the GnomAD database, including 13,216 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 0.42 (13216 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.880

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.422 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: 0.416 AC: 63204 AN: 151768 Hom.: 13188 Cov.: 30

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.417 AC: 63303 AN: 151886 Hom.: 13216 Cov.: 30 AF XY: 0.416 AC XY: 30893 AN XY: 74234

Gnomad4 AFR AF: 0.406

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.445

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.395

Gnomad4 NFE AF: 0.426

Gnomad4 OTH AF: 0.427

Alfa AF: 0.327 Hom.: 1232

Bravo AF: 0.419

Asia WGS AF: 0.457 AC: 1588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.72
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2748666; hg19: chr20-37405746;