rs12313471

Variant names:

• chr12-100470615-A-G
• rs12313471

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 0.179 in 152,170 control chromosomes in the GnomAD database, including 5,084 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 0.18 (5084 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.471 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: 0.179 AC: 27169 AN: 152052 Hom.: 5056 Cov.: 32

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.0881

Gnomad ASJ AF: 0.0799

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.0341

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0499

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.179 AC: 27240 AN: 152170 Hom.: 5084 Cov.: 32 AF XY: 0.176 AC XY: 13070 AN XY: 74412

African (AFR) AF: 0.476 AC: 19747 AN: 41468

American (AMR) AF: 0.0878 AC: 1343 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0799 AC: 277 AN: 3468

East Asian (EAS) AF: 0.178 AC: 919 AN: 5174

South Asian (SAS) AF: 0.180 AC: 865 AN: 4806

European-Finnish (FIN) AF: 0.0341 AC: 362 AN: 10616

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0499 AC: 3393 AN: 68030

Other (OTH) AF: 0.136 AC: 287 AN: 2110

Alfa AF: 0.0799 Hom.: 1561

Bravo AF: 0.197

Asia WGS AF: 0.189 AC: 659 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.1
DANN	Benign	0.31
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs12313471; hg19: chr12-100864393;