12-92496744-T-C

Position:

• chr12-92496744-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 0.914 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.92496744T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;