rs1974413

Variant names:

• chr21-45023971-G-A
• rs1974413

Your query was ambiguous. Multiple possible variants found:

• chr21-45023971-G-A
• chr21-45023971-G-C
• chr21-45023971-G-T

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 0.544 in 152,062 control chromosomes in the GnomAD database, including 24,672 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 0.54 (24672 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0750
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.544 AC: 82688 AN: 151944 Hom.: 24631 Cov.: 33

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.544 AC: 82782 AN: 152062 Hom.: 24672 Cov.: 33 AF XY: 0.543 AC XY: 40335 AN XY: 74324

African (AFR) AF: 0.802 AC: 33275 AN: 41498

American (AMR) AF: 0.562 AC: 8580 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1877 AN: 3472

East Asian (EAS) AF: 0.539 AC: 2792 AN: 5180

South Asian (SAS) AF: 0.412 AC: 1986 AN: 4824

European-Finnish (FIN) AF: 0.415 AC: 4384 AN: 10562

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

European-Non Finnish (NFE) AF: 0.414 AC: 28155 AN: 67940

Other (OTH) AF: 0.529 AC: 1117 AN: 2110

Alfa AF: 0.476 Hom.: 9105

Bravo AF: 0.570

Asia WGS AF: 0.462 AC: 1609 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.2
DANN	Benign	0.27
PhyloP100		-0.075

Splicing

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

Other links and lift over

dbSNP: rs1974413; hg19: chr21-46443886;