rs10507022

Positions:

• chr12-92987492-T-A
• chr12-92987492-T-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 0.047 in 152,196 control chromosomes in the GnomAD database, including 323 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 0.047 (323 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.413

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.103 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: 0.0468 AC: 7124 AN: 152076 Hom.: 315 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0166

Gnomad ASJ AF: 0.00548

Gnomad EAS AF: 0.0400

Gnomad SAS AF: 0.0676

Gnomad FIN AF: 0.0611

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0178

Gnomad OTH AF: 0.0354

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

GnomAD4 genome AF: 0.0470 AC: 7154 AN: 152196 Hom.: 323 Cov.: 32 AF XY: 0.0484 AC XY: 3601 AN XY: 74412

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.0166

Gnomad4 ASJ AF: 0.00548

Gnomad4 EAS AF: 0.0399

Gnomad4 SAS AF: 0.0679

Gnomad4 FIN AF: 0.0611

Gnomad4 NFE AF: 0.0178

Gnomad4 OTH AF: 0.0435

Alfa AF: 0.0147 Hom.: 12

Bravo AF: 0.0446

Asia WGS AF: 0.0850 AC: 297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	8.5
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10507022; hg19: chr12-93381268;