rs10496604

chr2-123028181-G-Achr2-123028181-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 0.667 in 151,926 control chromosomes in the GnomAD database, including 34,760 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 0.67 (34760 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.560

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.807 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: 0.667 AC: 101235 AN: 151810 Hom.: 34702 Cov.: 31

Gnomad AFR AF: 0.814

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.668

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

GnomAD4 genome AF: 0.667 AC: 101353 AN: 151926 Hom.: 34760 Cov.: 31 AF XY: 0.663 AC XY: 49239 AN XY: 74226

Gnomad4 AFR AF: 0.814

Gnomad4 AMR AF: 0.728

Gnomad4 ASJ AF: 0.645

Gnomad4 EAS AF: 0.697

Gnomad4 SAS AF: 0.544

Gnomad4 FIN AF: 0.509

Gnomad4 NFE AF: 0.596

Gnomad4 OTH AF: 0.671

Alfa AF: 0.487 Hom.: 1193

Bravo AF: 0.694

Asia WGS AF: 0.664 AC: 2310 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	0.21
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10496604; hg19: chr2-123785757;