rs1543400

Positions:

• chr20-40833953-C-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.432 in 152,066 control chromosomes in the GnomAD database, including 14,651 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 0.43 (14651 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.66

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.29).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.475 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: 0.431 AC: 65558 AN: 151946 Hom.: 14633 Cov.: 33

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.432 AC: 65621 AN: 152066 Hom.: 14651 Cov.: 33 AF XY: 0.429 AC XY: 31899 AN XY: 74308

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.526

Gnomad4 EAS AF: 0.211

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.544

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.436

Alfa AF: 0.462 Hom.: 2013

Bravo AF: 0.417

Asia WGS AF: 0.282 AC: 981 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	23
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1543400; hg19: chr20-39462593;