rs12408339

Variant names:

• chr1-156385718-G-A
• rs12408339

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 0.0933 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0895 AC: 3683 AN: 41164

American (AMR) AF: 0.0868 AC: 1321 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 466 AN: 3468

East Asian (EAS) AF: 0.172 AC: 859 AN: 4982

South Asian (SAS) AF: 0.184 AC: 882 AN: 4796

European-Finnish (FIN) AF: 0.0498 AC: 526 AN: 10572

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.0901 AC: 6123 AN: 67956

Other (OTH) AF: 0.0989 AC: 208 AN: 2104

Alfa AF: 0.0917 Hom.: 977

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
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs12408339; hg19: chr1-156355510;