rs12139150

Variant names:

• chr1-161500715-G-C
• rs12139150

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 0.424 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
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.365 AC: 15142 AN: 41444

American (AMR) AF: 0.401 AC: 6127 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1384 AN: 3472

East Asian (EAS) AF: 0.237 AC: 1223 AN: 5164

South Asian (SAS) AF: 0.398 AC: 1919 AN: 4826

European-Finnish (FIN) AF: 0.436 AC: 4615 AN: 10574

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.481 AC: 32676 AN: 67978

Other (OTH) AF: 0.438 AC: 925 AN: 2110

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
PhyloP100		0.94

Splicing

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

Other links and lift over

dbSNP: rs12139150; hg19: chr1-161470505;