12-107263540-G-A

Variant names:

• chr12-107263540-G-A
• rs6539316

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 0.334 in 152,118 control chromosomes in the GnomAD database, including 9,209 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 0.33 (9209 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.669
• Publications: 4 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 (NFE) allele frequency at 95% confidence interval = 0.397 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: 0.334 AC: 50772 AN: 152000 Hom.: 9195 Cov.: 33

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.334 AC: 50826 AN: 152118 Hom.: 9209 Cov.: 33 AF XY: 0.337 AC XY: 25050 AN XY: 74356

African (AFR) AF: 0.208 AC: 8641 AN: 41504

American (AMR) AF: 0.383 AC: 5849 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 949 AN: 3470

East Asian (EAS) AF: 0.186 AC: 962 AN: 5182

South Asian (SAS) AF: 0.321 AC: 1545 AN: 4820

European-Finnish (FIN) AF: 0.427 AC: 4503 AN: 10558

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.401 AC: 27246 AN: 67986

Other (OTH) AF: 0.346 AC: 730 AN: 2112

Alfa AF: 0.347 Hom.: 9559

Bravo AF: 0.323

Asia WGS AF: 0.231 AC: 803 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	0.60
DANN	Benign	0.56
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs6539316; hg19: chr12-107657318;