chr12-748335-A-C

Variant names:

• chr12-748335-A-C
• rs1468326

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.653 AC: 26729 AN: 40942

American (AMR) AF: 0.820 AC: 12389 AN: 15108

Ashkenazi Jewish (ASJ) AF: 0.814 AC: 2826 AN: 3470

East Asian (EAS) AF: 0.633 AC: 3227 AN: 5096

South Asian (SAS) AF: 0.820 AC: 3914 AN: 4772

European-Finnish (FIN) AF: 0.777 AC: 7988 AN: 10280

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.884 AC: 59915 AN: 67806

Other (OTH) AF: 0.795 AC: 1645 AN: 2068

Alfa AF: 0.857 Hom.: 63660

Bravo AF: 0.791

Asia WGS AF: 0.713 AC: 2481 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.4
DANN	Benign	0.76
PhyloP100		-0.30

Splicing

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

Other links and lift over

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