rs6101837

Positions:

• chr20-40093926-C-T

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 0.511 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

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 (EAS) allele frequency at 95% confidence interval = 0.588 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: 0.511 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

Gnomad4 AFR AF: 0.410

Gnomad4 AMR AF: 0.509

Gnomad4 ASJ AF: 0.522

Gnomad4 EAS AF: 0.606

Gnomad4 SAS AF: 0.548

Gnomad4 FIN AF: 0.518

Gnomad4 NFE AF: 0.562

Gnomad4 OTH AF: 0.521

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

Publications

LitVar

Other links and lift over

dbSNP: rs6101837; hg19: chr20-38722567;