chr21-44983382-G-A

Variant names:

• chr21-44983382-G-A
• rs12626362

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 0.047 in 25,154 control chromosomes in the GnomAD database, including 9 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 0.047 (9 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0706 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0471 AC: 1184 AN: 25134 Hom.: 9 Cov.: 32

Gnomad AFR AF: 0.0299

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0231

Gnomad ASJ AF: 0.0613

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00987

Gnomad FIN AF: 0.0400

Gnomad MID AF: 0.0690

Gnomad NFE AF: 0.0747

Gnomad OTH AF: 0.0395

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

GnomAD4 genome AF: 0.0470 AC: 1183 AN: 25154 Hom.: 9 Cov.: 32 AF XY: 0.0431 AC XY: 546 AN XY: 12656

African (AFR) AF: 0.0297 AC: 64 AN: 2152

American (AMR) AF: 0.0230 AC: 86 AN: 3732

Ashkenazi Jewish (ASJ) AF: 0.0613 AC: 57 AN: 930

East Asian (EAS) AF: 0.00 AC: 0 AN: 2774

South Asian (SAS) AF: 0.00985 AC: 14 AN: 1422

European-Finnish (FIN) AF: 0.0400 AC: 78 AN: 1950

Middle Eastern (MID) AF: 0.0556 AC: 3 AN: 54

European-Non Finnish (NFE) AF: 0.0747 AC: 864 AN: 11566

Other (OTH) AF: 0.0394 AC: 17 AN: 432

Alfa AF: 0.00 Hom.: 3

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.0
DANN	Benign	0.65
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs12626362; hg19: chr21-46403297;