rs12439270

Variant names:

• chr15-59949881-C-A
• rs12439270

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 0.299 in 152,054 control chromosomes in the GnomAD database, including 7,988 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 0.30 (7988 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.426
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.477 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: 0.299 AC: 45474 AN: 151936 Hom.: 7982 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.299 AC: 45486 AN: 152054 Hom.: 7988 Cov.: 32 AF XY: 0.298 AC XY: 22140 AN XY: 74340

African (AFR) AF: 0.142 AC: 5890 AN: 41502

American (AMR) AF: 0.486 AC: 7411 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1180 AN: 3472

East Asian (EAS) AF: 0.137 AC: 709 AN: 5162

South Asian (SAS) AF: 0.196 AC: 946 AN: 4822

European-Finnish (FIN) AF: 0.304 AC: 3215 AN: 10568

Middle Eastern (MID) AF: 0.247 AC: 72 AN: 292

European-Non Finnish (NFE) AF: 0.367 AC: 24970 AN: 67964

Other (OTH) AF: 0.312 AC: 661 AN: 2116

Alfa AF: 0.345 Hom.: 31059

Bravo AF: 0.313

Asia WGS AF: 0.161 AC: 559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.4
DANN	Benign	0.25
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs12439270; hg19: chr15-60242080;