21-43044602-T-C

Variant names:

• chr21-43044602-T-C
• rs400660

Variant summary

Our verdict is Likely benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

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

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: 0.724 AC: 48631 AN: 67200 Hom.: 20355 Cov.: 9

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

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.733 AC: 14102 AN: 19232

American (AMR) AF: 0.663 AC: 5064 AN: 7638

Ashkenazi Jewish (ASJ) AF: 0.735 AC: 1365 AN: 1856

East Asian (EAS) AF: 0.640 AC: 1907 AN: 2978

South Asian (SAS) AF: 0.640 AC: 1135 AN: 1774

European-Finnish (FIN) AF: 0.671 AC: 2415 AN: 3598

Middle Eastern (MID) AF: 0.675 AC: 104 AN: 154

European-Non Finnish (NFE) AF: 0.757 AC: 21784 AN: 28776

Other (OTH) AF: 0.651 AC: 603 AN: 926

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.882 Hom.: 9928

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
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs400660; hg19: chr21-44464712;