rs12907270

Variant names:

• chr15-85819933-C-G
• rs12907270

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 0.124 in 152,136 control chromosomes in the GnomAD database, including 1,449 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 0.12 (1449 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22
• 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 (SAS) allele frequency at 95% confidence interval = 0.289 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: 0.124 AC: 18871 AN: 152016 Hom.: 1447 Cov.: 33

Gnomad AFR AF: 0.0785

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.0994

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.0855

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.124 AC: 18874 AN: 152136 Hom.: 1449 Cov.: 33 AF XY: 0.125 AC XY: 9278 AN XY: 74350

African (AFR) AF: 0.0784 AC: 3253 AN: 41486

American (AMR) AF: 0.0993 AC: 1515 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 671 AN: 3472

East Asian (EAS) AF: 0.212 AC: 1095 AN: 5168

South Asian (SAS) AF: 0.302 AC: 1455 AN: 4824

European-Finnish (FIN) AF: 0.0855 AC: 906 AN: 10596

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.137 AC: 9344 AN: 68020

Other (OTH) AF: 0.137 AC: 290 AN: 2112

Alfa AF: 0.120 Hom.: 157

Bravo AF: 0.122

Asia WGS AF: 0.221 AC: 766 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	3.8
DANN	Benign	0.45
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs12907270; hg19: chr15-86363164;