rs12408339

Positions:

• chr1-156385718-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;