21-40977447-T-C

Variant names:

• chr21-40977447-T-C
• rs713112

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.527 in 151,818 control chromosomes in the GnomAD database, including 22,232 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 0.53 (22232 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

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: 0.527 AC: 79939 AN: 151700 Hom.: 22177 Cov.: 31

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.527 AC: 80057 AN: 151818 Hom.: 22232 Cov.: 31 AF XY: 0.524 AC XY: 38894 AN XY: 74198

African (AFR) AF: 0.695 AC: 28768 AN: 41378

American (AMR) AF: 0.585 AC: 8922 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1707 AN: 3466

East Asian (EAS) AF: 0.313 AC: 1612 AN: 5142

South Asian (SAS) AF: 0.403 AC: 1934 AN: 4802

European-Finnish (FIN) AF: 0.453 AC: 4784 AN: 10554

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.451 AC: 30594 AN: 67894

Other (OTH) AF: 0.534 AC: 1128 AN: 2114

Alfa AF: 0.492 Hom.: 3091

Bravo AF: 0.549

Asia WGS AF: 0.402 AC: 1398 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.50
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs713112; hg19: chr21-42349373;