rs10492232

Positions:

• chr12-91074619-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 0.132 in 152,144 control chromosomes in the GnomAD database, including 1,497 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 0.13 (1497 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.557

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19985 AN: 152026 Hom.: 1489 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.0871

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.0707

Gnomad SAS AF: 0.0663

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.132 AC: 20017 AN: 152144 Hom.: 1497 Cov.: 32 AF XY: 0.129 AC XY: 9620 AN XY: 74402

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.0874

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.0707

Gnomad4 SAS AF: 0.0665

Gnomad4 FIN AF: 0.100

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.123

Alfa AF: 0.114 Hom.: 341

Bravo AF: 0.135

Asia WGS AF: 0.0720 AC: 252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	13
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10492232; hg19: chr12-91468396;