12-92496744-T-C

Variant names:

• chr12-92496744-T-C
• rs10219495

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 0.914 in 152,278 control chromosomes in the GnomAD database, including 63,704 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 0.91 (63704 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 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: 0.914 AC: 139058 AN: 152160 Hom.: 63638 Cov.: 32

Gnomad AFR AF: 0.967

Gnomad AMI AF: 0.901

Gnomad AMR AF: 0.923

Gnomad ASJ AF: 0.866

Gnomad EAS AF: 0.993

Gnomad SAS AF: 0.885

Gnomad FIN AF: 0.895

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.882

Gnomad OTH AF: 0.906

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

GnomAD4 genome AF: 0.914 AC: 139186 AN: 152278 Hom.: 63704 Cov.: 32 AF XY: 0.914 AC XY: 68046 AN XY: 74450

Gnomad4 AFR AF: 0.967

Gnomad4 AMR AF: 0.923

Gnomad4 ASJ AF: 0.866

Gnomad4 EAS AF: 0.993

Gnomad4 SAS AF: 0.886

Gnomad4 FIN AF: 0.895

Gnomad4 NFE AF: 0.882

Gnomad4 OTH AF: 0.906

Alfa AF: 0.891 Hom.: 76885

Bravo AF: 0.920

Asia WGS AF: 0.934 AC: 3246 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.0
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10219495; hg19: chr12-92890520;