12-748335-A-C

Position:

• chr12-748335-A-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 0.794 in 150,748 control chromosomes in the GnomAD database, including 48,263 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 0.79 (48263 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.301

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.878 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: 0.794 AC: 119658 AN: 150630 Hom.: 48252 Cov.: 25

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.907

Gnomad AMR AF: 0.820

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.633

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.777

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.884

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.794 AC: 119706 AN: 150748 Hom.: 48263 Cov.: 25 AF XY: 0.791 AC XY: 58208 AN XY: 73594

Gnomad4 AFR AF: 0.653

Gnomad4 AMR AF: 0.820

Gnomad4 ASJ AF: 0.814

Gnomad4 EAS AF: 0.633

Gnomad4 SAS AF: 0.820

Gnomad4 FIN AF: 0.777

Gnomad4 NFE AF: 0.884

Gnomad4 OTH AF: 0.795

Alfa AF: 0.865 Hom.: 49084

Bravo AF: 0.791

Asia WGS AF: 0.713 AC: 2481 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.4
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1468326; hg19: chr12-857501; COSMIC: COSV60037608;