1-156143270-G-A

Variant names:

• chr1-156143270-G-A
• rs12063072

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 0.0748 in 151,330 control chromosomes in the GnomAD database, including 870 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 0.075 (870 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0748 AC: 11313 AN: 151214 Hom.: 870 Cov.: 30

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.0606

Gnomad AMR AF: 0.0318

Gnomad ASJ AF: 0.0396

Gnomad EAS AF: 0.0221

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0266

Gnomad MID AF: 0.0350

Gnomad NFE AF: 0.0260

Gnomad OTH AF: 0.0543

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

GnomAD4 genome AF: 0.0748 AC: 11325 AN: 151330 Hom.: 870 Cov.: 30 AF XY: 0.0732 AC XY: 5407 AN XY: 73872

African (AFR) AF: 0.191 AC: 7892 AN: 41250

American (AMR) AF: 0.0318 AC: 483 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.0396 AC: 137 AN: 3462

East Asian (EAS) AF: 0.0219 AC: 111 AN: 5060

South Asian (SAS) AF: 0.101 AC: 485 AN: 4786

European-Finnish (FIN) AF: 0.0266 AC: 277 AN: 10400

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0259 AC: 1761 AN: 67864

Other (OTH) AF: 0.0542 AC: 114 AN: 2104

Alfa AF: 0.0354 Hom.: 91

Bravo AF: 0.0774

Asia WGS AF: 0.0650 AC: 224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.0
DANN	Benign	0.58
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs12063072; hg19: chr1-156113061;