rs12145940

Variant names:

• chr1-208644861-C-A
• rs12145940

Your query was ambiguous. Multiple possible variants found:

• chr1-208644861-C-A
• chr1-208644861-C-G
• chr1-208644861-C-T

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 0.589 in 149,672 control chromosomes in the GnomAD database, including 28,027 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 0.59 (28027 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.463
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.773 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: 0.589 AC: 88081 AN: 149560 Hom.: 28018 Cov.: 25

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.727

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.737

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.794

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.589 AC: 88111 AN: 149672 Hom.: 28027 Cov.: 25 AF XY: 0.590 AC XY: 43068 AN XY: 72952

African (AFR) AF: 0.319 AC: 12883 AN: 40446

American (AMR) AF: 0.716 AC: 10748 AN: 15012

Ashkenazi Jewish (ASJ) AF: 0.737 AC: 2547 AN: 3458

East Asian (EAS) AF: 0.759 AC: 3831 AN: 5048

South Asian (SAS) AF: 0.795 AC: 3720 AN: 4682

European-Finnish (FIN) AF: 0.593 AC: 6034 AN: 10172

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.683 AC: 46165 AN: 67592

Other (OTH) AF: 0.640 AC: 1318 AN: 2060

Alfa AF: 0.639 Hom.: 67104

Bravo AF: 0.583

Asia WGS AF: 0.727 AC: 2526 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.9
DANN	Benign	0.52
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs12145940; hg19: chr1-208818206;