12-9321129-A-G

Variant names:

• chr12-9321129-A-G
• rs7311758

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 0.538 in 151,186 control chromosomes in the GnomAD database, including 22,194 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 0.54 (22194 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.978
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.716 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: 0.538 AC: 81241 AN: 151070 Hom.: 22152 Cov.: 30

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.538 AC: 81332 AN: 151186 Hom.: 22194 Cov.: 30 AF XY: 0.545 AC XY: 40243 AN XY: 73860

African (AFR) AF: 0.570 AC: 23469 AN: 41158

American (AMR) AF: 0.577 AC: 8773 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.539 AC: 1866 AN: 3460

East Asian (EAS) AF: 0.293 AC: 1507 AN: 5140

South Asian (SAS) AF: 0.736 AC: 3532 AN: 4796

European-Finnish (FIN) AF: 0.592 AC: 6205 AN: 10486

Middle Eastern (MID) AF: 0.507 AC: 146 AN: 288

European-Non Finnish (NFE) AF: 0.507 AC: 34275 AN: 67656

Other (OTH) AF: 0.509 AC: 1069 AN: 2100

Alfa AF: 0.536 Hom.: 2652

Bravo AF: 0.532

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.44
DANN	Benign	0.067
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs7311758; hg19: chr12-9473725;