rs12408339

Variant names:

• chr1-156385718-G-A
• rs12408339

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0933 in 151,464 control chromosomes in the GnomAD database, including 748 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 0.093 (748 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.478

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.174 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: 0.0933 AC: 14121 AN: 151346 Hom.: 748 Cov.: 31

Gnomad AFR AF: 0.0897

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0867

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.0498

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0901

Gnomad OTH AF: 0.0980

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

GnomAD4 genome AF: 0.0933 AC: 14129 AN: 151464 Hom.: 748 Cov.: 31 AF XY: 0.0939 AC XY: 6950 AN XY: 74050

Gnomad4 AFR AF: 0.0895

Gnomad4 AMR AF: 0.0868

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.0498

Gnomad4 NFE AF: 0.0901

Gnomad4 OTH AF: 0.0989

Alfa AF: 0.0892 Hom.: 77

Bravo AF: 0.0941

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.5
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12408339; hg19: chr1-156355510;