rs731059

chr21-33902813-G-Tchr21-33902813-G-C

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 0.32 in 152,084 control chromosomes in the GnomAD database, including 7,843 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 0.32 (7843 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.379 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: 0.320 AC: 48612 AN: 151964 Hom.: 7841 Cov.: 32

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.320 AC: 48636 AN: 152084 Hom.: 7843 Cov.: 32 AF XY: 0.320 AC XY: 23782 AN XY: 74332

Gnomad4 AFR AF: 0.384

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.343

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.287

Alfa AF: 0.296 Hom.: 12724

Bravo AF: 0.318

Asia WGS AF: 0.330 AC: 1147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.22
Dann	Benign	0.85

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs731059; hg19: chr21-35275117;