12-92698941-C-T

Variant names:

• chr12-92698941-C-T
• rs7316876

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 0.447 in 152,018 control chromosomes in the GnomAD database, including 16,533 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 0.45 (16533 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.871 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: 0.447 AC: 67909 AN: 151900 Hom.: 16504 Cov.: 32

Gnomad AFR AF: 0.534

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.892

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.447 AC: 67989 AN: 152018 Hom.: 16533 Cov.: 32 AF XY: 0.455 AC XY: 33792 AN XY: 74298

African (AFR) AF: 0.533 AC: 22109 AN: 41448

American (AMR) AF: 0.573 AC: 8756 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1543 AN: 3472

East Asian (EAS) AF: 0.892 AC: 4626 AN: 5184

South Asian (SAS) AF: 0.542 AC: 2613 AN: 4824

European-Finnish (FIN) AF: 0.340 AC: 3585 AN: 10536

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.344 AC: 23406 AN: 67968

Other (OTH) AF: 0.458 AC: 967 AN: 2110

Alfa AF: 0.396 Hom.: 42980

Bravo AF: 0.477

Asia WGS AF: 0.710 AC: 2465 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.11
DANN	Benign	0.19
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs7316876; hg19: chr12-93092717;