rs12316797

Variant names:

• chr12-42766942-T-G
• rs12316797

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 0.183 in 152,150 control chromosomes in the GnomAD database, including 2,958 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 (2958 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.100
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.257 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: 0.183 AC: 27873 AN: 152032 Hom.: 2953 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.183 AC: 27901 AN: 152150 Hom.: 2958 Cov.: 32 AF XY: 0.186 AC XY: 13839 AN XY: 74384

African (AFR) AF: 0.261 AC: 10837 AN: 41464

American (AMR) AF: 0.230 AC: 3516 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 399 AN: 3470

East Asian (EAS) AF: 0.268 AC: 1387 AN: 5170

South Asian (SAS) AF: 0.144 AC: 695 AN: 4824

European-Finnish (FIN) AF: 0.158 AC: 1679 AN: 10606

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8671 AN: 68020

Other (OTH) AF: 0.178 AC: 376 AN: 2112

Alfa AF: 0.145 Hom.: 6905

Bravo AF: 0.196

Asia WGS AF: 0.214 AC: 742 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.6
DANN	Benign	0.49
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs12316797; hg19: chr12-43160744;