12-12270159-G-A

Variant names:

• chr12-12270159-G-A
• rs7136900

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 0.347 in 151,958 control chromosomes in the GnomAD database, including 9,657 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 0.35 (9657 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.227
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.419 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: 0.347 AC: 52647 AN: 151840 Hom.: 9649 Cov.: 31

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.0811

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.347 AC: 52689 AN: 151958 Hom.: 9657 Cov.: 31 AF XY: 0.342 AC XY: 25363 AN XY: 74234

African (AFR) AF: 0.424 AC: 17581 AN: 41442

American (AMR) AF: 0.288 AC: 4396 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1172 AN: 3468

East Asian (EAS) AF: 0.0813 AC: 420 AN: 5166

South Asian (SAS) AF: 0.193 AC: 931 AN: 4820

European-Finnish (FIN) AF: 0.334 AC: 3508 AN: 10510

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.345 AC: 23430 AN: 67986

Other (OTH) AF: 0.358 AC: 756 AN: 2110

Alfa AF: 0.346 Hom.: 32045

Bravo AF: 0.351

Asia WGS AF: 0.158 AC: 554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	4.6
DANN	Benign	0.76
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs7136900; hg19: chr12-12423093;