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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.544 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

Gnomad4 AFR AF: 0.802

Gnomad4 AMR AF: 0.562

Gnomad4 ASJ AF: 0.541

Gnomad4 EAS AF: 0.539

Gnomad4 SAS AF: 0.412

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.414

Gnomad4 OTH AF: 0.529

Alfa AF: 0.472 Hom.: 7599

Bravo AF: 0.570

Asia WGS AF: 0.462 AC: 1609 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	1.2
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1974413; hg19: chr21-46443886;