rs10496601

chr2-122895707-A-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 0.0355 in 151,940 control chromosomes in the GnomAD database, including 249 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 0.036 (249 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178

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 = 0.0993 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: 0.0355 AC: 5389 AN: 151822 Hom.: 246 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0180

Gnomad ASJ AF: 0.0769

Gnomad EAS AF: 0.00233

Gnomad SAS AF: 0.0685

Gnomad FIN AF: 0.0000941

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.00320

Gnomad OTH AF: 0.0306

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

GnomAD4 genome AF: 0.0355 AC: 5398 AN: 151940 Hom.: 249 Cov.: 32 AF XY: 0.0354 AC XY: 2627 AN XY: 74278

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.0180

Gnomad4 ASJ AF: 0.0769

Gnomad4 EAS AF: 0.00233

Gnomad4 SAS AF: 0.0686

Gnomad4 FIN AF: 0.0000941

Gnomad4 NFE AF: 0.00320

Gnomad4 OTH AF: 0.0303

Alfa AF: 0.0217 Hom.: 39

Bravo AF: 0.0385

Asia WGS AF: 0.0450 AC: 157 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	4.4
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10496601; hg19: chr2-123653283;