12-7582723-G-T

Variant names:

• chr12-7582723-G-T
• rs11054623

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 0.0696 in 148,018 control chromosomes in the GnomAD database, including 525 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 0.070 (525 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0925 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: 0.0696 AC: 10297 AN: 147896 Hom.: 525 Cov.: 32

Gnomad AFR AF: 0.0227

Gnomad AMI AF: 0.0531

Gnomad AMR AF: 0.0392

Gnomad ASJ AF: 0.0427

Gnomad EAS AF: 0.0176

Gnomad SAS AF: 0.0662

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.0573

Gnomad NFE AF: 0.0944

Gnomad OTH AF: 0.0578

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

GnomAD4 genome AF: 0.0696 AC: 10305 AN: 148018 Hom.: 525 Cov.: 32 AF XY: 0.0728 AC XY: 5260 AN XY: 72226

African (AFR) AF: 0.0227 AC: 939 AN: 41280

American (AMR) AF: 0.0393 AC: 588 AN: 14980

Ashkenazi Jewish (ASJ) AF: 0.0427 AC: 142 AN: 3328

East Asian (EAS) AF: 0.0177 AC: 84 AN: 4756

South Asian (SAS) AF: 0.0672 AC: 290 AN: 4318

European-Finnish (FIN) AF: 0.181 AC: 1870 AN: 10352

Middle Eastern (MID) AF: 0.0616 AC: 18 AN: 292

European-Non Finnish (NFE) AF: 0.0944 AC: 6208 AN: 65746

Other (OTH) AF: 0.0572 AC: 118 AN: 2062

Alfa AF: 0.0759 Hom.: 755

Bravo AF: 0.0552

Asia WGS AF: 0.0370 AC: 127 AN: 3422

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.22
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs11054623; hg19: chr12-7735319;