rs12143180

Variant names:

• chr1-161221765-G-A
• rs12143180

Your query was ambiguous. Multiple possible variants found:

• chr1-161221765-G-A
• chr1-161221765-G-C

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 0.161 in 137,912 control chromosomes in the GnomAD database, including 1,899 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 0.16 (1899 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.722
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.318 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: 0.161 AC: 22255 AN: 137852 Hom.: 1900 Cov.: 27

Gnomad AFR AF: 0.0897

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.161 AC: 22241 AN: 137912 Hom.: 1899 Cov.: 27 AF XY: 0.162 AC XY: 10706 AN XY: 66028

African (AFR) AF: 0.0897 AC: 3238 AN: 36084

American (AMR) AF: 0.250 AC: 3228 AN: 12928

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 704 AN: 3426

East Asian (EAS) AF: 0.332 AC: 1542 AN: 4646

South Asian (SAS) AF: 0.151 AC: 622 AN: 4126

European-Finnish (FIN) AF: 0.140 AC: 1093 AN: 7826

Middle Eastern (MID) AF: 0.204 AC: 49 AN: 240

European-Non Finnish (NFE) AF: 0.171 AC: 11292 AN: 65854

Other (OTH) AF: 0.179 AC: 338 AN: 1892

Alfa AF: 0.140 Hom.: 210

Bravo AF: 0.153

Asia WGS AF: 0.240 AC: 832 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.0
DANN	Benign	0.28
PhyloP100		-0.72

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs12143180; hg19: chr1-161191555;