chr20-40093926-C-T

Variant names:

• chr20-40093926-C-T
• rs6101837

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 0.511 in 152,026 control chromosomes in the GnomAD database, including 20,332 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 0.51 (20332 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.588 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: 0.511 AC: 77689 AN: 151906 Hom.: 20315 Cov.: 32

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.511 AC: 77758 AN: 152026 Hom.: 20332 Cov.: 32 AF XY: 0.511 AC XY: 37994 AN XY: 74292

African (AFR) AF: 0.410 AC: 17025 AN: 41478

American (AMR) AF: 0.509 AC: 7772 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1811 AN: 3468

East Asian (EAS) AF: 0.606 AC: 3118 AN: 5146

South Asian (SAS) AF: 0.548 AC: 2641 AN: 4822

European-Finnish (FIN) AF: 0.518 AC: 5479 AN: 10572

Middle Eastern (MID) AF: 0.466 AC: 136 AN: 292

European-Non Finnish (NFE) AF: 0.562 AC: 38175 AN: 67948

Other (OTH) AF: 0.521 AC: 1099 AN: 2108

Alfa AF: 0.537 Hom.: 2715

Bravo AF: 0.507

Asia WGS AF: 0.538 AC: 1874 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	2.5
DANN	Benign	0.92

Splicing

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

Other links and lift over

dbSNP: rs6101837; hg19: chr20-38722567;