rs2748666

Variant names:

• chr20-38777103-T-C
• rs2748666

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;