rs12113442

chr7-146001098-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.184 in 152,018 control chromosomes in the GnomAD database, including 3,063 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 (3063 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.333

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.184 AC: 27932 AN: 151898 Hom.: 3047 Cov.: 32

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.184 AC: 27990 AN: 152018 Hom.: 3063 Cov.: 32 AF XY: 0.182 AC XY: 13562 AN XY: 74328

Gnomad4 AFR AF: 0.306

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.121

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.167

Alfa AF: 0.172 Hom.: 547

Bravo AF: 0.188

Asia WGS AF: 0.161 AC: 561 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.0
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12113442; hg19: chr7-145698191;