rs7316408

Variant names:

• chr12-117979974-A-G
• rs7316408

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 0.292 in 151,966 control chromosomes in the GnomAD database, including 7,013 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 0.29 (7013 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.99
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.359 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: 0.292 AC: 44368 AN: 151848 Hom.: 7014 Cov.: 31

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.292 AC: 44379 AN: 151966 Hom.: 7013 Cov.: 31 AF XY: 0.290 AC XY: 21517 AN XY: 74258

African (AFR) AF: 0.174 AC: 7219 AN: 41470

American (AMR) AF: 0.247 AC: 3774 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 985 AN: 3468

East Asian (EAS) AF: 0.343 AC: 1772 AN: 5162

South Asian (SAS) AF: 0.209 AC: 1006 AN: 4818

European-Finnish (FIN) AF: 0.373 AC: 3929 AN: 10538

Middle Eastern (MID) AF: 0.329 AC: 96 AN: 292

European-Non Finnish (NFE) AF: 0.362 AC: 24622 AN: 67944

Other (OTH) AF: 0.306 AC: 646 AN: 2110

Alfa AF: 0.347 Hom.: 2767

Bravo AF: 0.279

Asia WGS AF: 0.266 AC: 921 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.7
DANN	Benign	0.88
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs7316408; hg19: chr12-118417779;