rs1475591

Variant names:

• chr21-31068221-T-C
• rs1475591

Your query was ambiguous. Multiple possible variants found:

• chr21-31068221-T-C
• chr21-31068221-T-G

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 0.848 in 152,232 control chromosomes in the GnomAD database, including 56,781 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 0.85 (56781 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.95 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: 0.849 AC: 129075 AN: 152114 Hom.: 56772 Cov.: 33

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.970

Gnomad AMR AF: 0.923

Gnomad ASJ AF: 0.940

Gnomad EAS AF: 0.917

Gnomad SAS AF: 0.898

Gnomad FIN AF: 0.964

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.956

Gnomad OTH AF: 0.883

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

GnomAD4 genome AF: 0.848 AC: 129120 AN: 152232 Hom.: 56781 Cov.: 33 AF XY: 0.850 AC XY: 63247 AN XY: 74436

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.923

Gnomad4 ASJ AF: 0.940

Gnomad4 EAS AF: 0.917

Gnomad4 SAS AF: 0.899

Gnomad4 FIN AF: 0.964

Gnomad4 NFE AF: 0.956

Gnomad4 OTH AF: 0.883

Alfa AF: 0.944 Hom.: 116228

Bravo AF: 0.837

Asia WGS AF: 0.893 AC: 3105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.032
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1475591; hg19: chr21-32440540;