rs1524668

Positions:

• chr2-9557243-A-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 0.63 in 151,838 control chromosomes in the GnomAD database, including 31,513 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).

• Frequency: Genomes: 𝑓 0.63 (31513 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08

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 (AFR) allele frequency at 95% confidence interval = 0.707 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.630 AC: 95527 AN: 151720 Hom.: 31482 Cov.: 30

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.851

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.0927

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.758

Gnomad NFE AF: 0.672

Gnomad OTH AF: 0.653

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

GnomAD4 genome AF: 0.630 AC: 95603 AN: 151838 Hom.: 31513 Cov.: 30 AF XY: 0.615 AC XY: 45581 AN XY: 74132

Gnomad4 AFR AF: 0.714

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.690

Gnomad4 EAS AF: 0.0923

Gnomad4 SAS AF: 0.448

Gnomad4 FIN AF: 0.529

Gnomad4 NFE AF: 0.672

Gnomad4 OTH AF: 0.649

Alfa AF: 0.645 Hom.: 11182

Bravo AF: 0.628

Asia WGS AF: 0.315 AC: 1097 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	0.46
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1524668; hg19: chr2-9697372;