rs12242110

chr10-35246767-A-Gchr10-35246767-A-T

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 0.323 in 152,076 control chromosomes in the GnomAD database, including 8,031 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 (8031 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390

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 = 0.33 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: 0.323 AC: 49014 AN: 151958 Hom.: 8017 Cov.: 32

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.323 AC: 49066 AN: 152076 Hom.: 8031 Cov.: 32 AF XY: 0.324 AC XY: 24078 AN XY: 74334

Gnomad4 AFR AF: 0.335

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.298

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.353

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.342

Alfa AF: 0.322 Hom.: 14768

Bravo AF: 0.317

Asia WGS AF: 0.344 AC: 1193 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	0.14
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12242110; hg19: chr10-35535695;