rs1041456

Positions:

• chr21-43786474-T-C
• chr21-43786474-T-A

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 0.574 in 151,904 control chromosomes in the GnomAD database, including 27,125 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 0.57 (27125 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.593

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.09).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.783 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: 0.574 AC: 87049 AN: 151784 Hom.: 27074 Cov.: 31

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.760

Gnomad SAS AF: 0.725

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.574 AC: 87154 AN: 151904 Hom.: 27125 Cov.: 31 AF XY: 0.580 AC XY: 43093 AN XY: 74248

Gnomad4 AFR AF: 0.790

Gnomad4 AMR AF: 0.635

Gnomad4 ASJ AF: 0.482

Gnomad4 EAS AF: 0.760

Gnomad4 SAS AF: 0.723

Gnomad4 FIN AF: 0.472

Gnomad4 NFE AF: 0.424

Gnomad4 OTH AF: 0.560

Alfa AF: 0.445 Hom.: 14447

Bravo AF: 0.595

Asia WGS AF: 0.748 AC: 2601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.77
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1041456; hg19: chr21-45206355;