rs12143180

chr1-161221765-G-Achr1-161221765-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 0.161 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0897

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.332

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.179

Alfa AF: 0.142 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

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

Publications

LitVar

Other links and lift over

dbSNP: rs12143180; hg19: chr1-161191555;