rs400660

chr21-43044602-T-Cchr21-43044602-T-Gchr21-43044602-T-A

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

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 0.72 (20376 hom., cov: 9)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

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: 0.00 AC: 48631 AN: 67200 Hom.: 20355 Cov.: 9 FAILED QC

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.608

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.679

Gnomad NFE AF: 0.757

Gnomad OTH AF: 0.660

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.724 AC: 48688 AN: 67276 Hom.: 20376 Cov.: 9 AF XY: 0.708 AC XY: 22591 AN XY: 31916

Gnomad4 AFR AF: 0.733

Gnomad4 AMR AF: 0.663

Gnomad4 ASJ AF: 0.735

Gnomad4 EAS AF: 0.640

Gnomad4 SAS AF: 0.640

Gnomad4 FIN AF: 0.671

Gnomad4 NFE AF: 0.757

Gnomad4 OTH AF: 0.651

Alfa AF: 0.883 Hom.: 9653

Asia WGS AF: 0.801 AC: 2786 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.7
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs400660; hg19: chr21-44464712;