12-92987492-T-A

Variant names:

• chr12-92987492-T-A
• rs10507022

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;