rs12757998

Variant names:

• chr1-182569343-C-T
• rs12757998

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 0.234 in 151,410 control chromosomes in the GnomAD database, including 4,706 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 0.23 (4706 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.602
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35404 AN: 151292 Hom.: 4703 Cov.: 28

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.00483

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.234 AC: 35408 AN: 151410 Hom.: 4706 Cov.: 28 AF XY: 0.234 AC XY: 17317 AN XY: 73920

African (AFR) AF: 0.143 AC: 5884 AN: 41264

American (AMR) AF: 0.231 AC: 3507 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 665 AN: 3460

East Asian (EAS) AF: 0.00484 AC: 25 AN: 5166

South Asian (SAS) AF: 0.157 AC: 752 AN: 4784

European-Finnish (FIN) AF: 0.351 AC: 3653 AN: 10402

Middle Eastern (MID) AF: 0.164 AC: 48 AN: 292

European-Non Finnish (NFE) AF: 0.298 AC: 20192 AN: 67856

Other (OTH) AF: 0.227 AC: 475 AN: 2092

Alfa AF: 0.264 Hom.: 3696

Bravo AF: 0.219

Asia WGS AF: 0.0950 AC: 331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.36
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs12757998; hg19: chr1-182538478;