12-43573874-T-G

Variant names:

• chr12-43573874-T-G
• rs7295246

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 0.376 in 152,064 control chromosomes in the GnomAD database, including 11,175 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 0.38 (11175 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.45 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: 0.376 AC: 57206 AN: 151946 Hom.: 11164 Cov.: 33

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.376 AC: 57250 AN: 152064 Hom.: 11175 Cov.: 33 AF XY: 0.377 AC XY: 28012 AN XY: 74316

African (AFR) AF: 0.332 AC: 13774 AN: 41468

American (AMR) AF: 0.279 AC: 4270 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1524 AN: 3464

East Asian (EAS) AF: 0.155 AC: 802 AN: 5174

South Asian (SAS) AF: 0.466 AC: 2246 AN: 4822

European-Finnish (FIN) AF: 0.449 AC: 4739 AN: 10554

Middle Eastern (MID) AF: 0.476 AC: 139 AN: 292

European-Non Finnish (NFE) AF: 0.420 AC: 28519 AN: 67974

Other (OTH) AF: 0.374 AC: 789 AN: 2112

Alfa AF: 0.381 Hom.: 3395

Bravo AF: 0.358

Asia WGS AF: 0.301 AC: 1048 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.7
DANN	Benign	0.72
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs7295246; hg19: chr12-43967677;