rs1513737

Positions:

• chr21-22793823-T-C
• chr21-22793823-T-A

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 0.616 in 151,964 control chromosomes in the GnomAD database, including 29,673 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 0.62 (29673 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.616 AC: 93530 AN: 151846 Hom.: 29620 Cov.: 31

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.694

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.616 AC: 93647 AN: 151964 Hom.: 29673 Cov.: 31 AF XY: 0.620 AC XY: 46007 AN XY: 74256

Gnomad4 AFR AF: 0.773

Gnomad4 AMR AF: 0.636

Gnomad4 ASJ AF: 0.550

Gnomad4 EAS AF: 0.560

Gnomad4 SAS AF: 0.695

Gnomad4 FIN AF: 0.541

Gnomad4 NFE AF: 0.532

Gnomad4 OTH AF: 0.604

Alfa AF: 0.549 Hom.: 42229

Bravo AF: 0.624

Asia WGS AF: 0.640 AC: 2225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.035
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1513737; hg19: chr21-24166144;