rs12967135

Variant names:

• chr18-60181790-G-A
• rs12967135

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 0.236 in 151,926 control chromosomes in the GnomAD database, including 4,402 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 0.24 (4402 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.664
• Publications: 92 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.338 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: 0.236 AC: 35879 AN: 151810 Hom.: 4400 Cov.: 33

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.295

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.236 AC: 35917 AN: 151926 Hom.: 4402 Cov.: 33 AF XY: 0.233 AC XY: 17300 AN XY: 74246

African (AFR) AF: 0.278 AC: 11538 AN: 41432

American (AMR) AF: 0.159 AC: 2436 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 696 AN: 3462

East Asian (EAS) AF: 0.184 AC: 952 AN: 5176

South Asian (SAS) AF: 0.352 AC: 1696 AN: 4822

European-Finnish (FIN) AF: 0.172 AC: 1809 AN: 10530

Middle Eastern (MID) AF: 0.293 AC: 85 AN: 290

European-Non Finnish (NFE) AF: 0.235 AC: 15953 AN: 67916

Other (OTH) AF: 0.224 AC: 472 AN: 2110

Alfa AF: 0.242 Hom.: 6004

Bravo AF: 0.235

Asia WGS AF: 0.226 AC: 786 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	4.4
DANN	Benign	0.86
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs12967135; hg19: chr18-57849023;