rs12139150

Positions:

• chr1-161500715-G-C

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 0.424 in 152,060 control chromosomes in the GnomAD database, including 14,065 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 0.42 (14065 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.936

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64422 AN: 151942 Hom.: 14069 Cov.: 32

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.424 AC: 64450 AN: 152060 Hom.: 14065 Cov.: 32 AF XY: 0.418 AC XY: 31108 AN XY: 74342

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.401

Gnomad4 ASJ AF: 0.399

Gnomad4 EAS AF: 0.237

Gnomad4 SAS AF: 0.398

Gnomad4 FIN AF: 0.436

Gnomad4 NFE AF: 0.481

Gnomad4 OTH AF: 0.438

Alfa AF: 0.446 Hom.: 1905

Bravo AF: 0.423

Asia WGS AF: 0.328 AC: 1144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.9
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12139150; hg19: chr1-161470505;