rs12113442

Variant names:

• chr7-146001098-T-G
• rs12113442

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 0.184 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.306 AC: 12704 AN: 41478

American (AMR) AF: 0.127 AC: 1938 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 376 AN: 3470

East Asian (EAS) AF: 0.176 AC: 903 AN: 5126

South Asian (SAS) AF: 0.178 AC: 861 AN: 4828

European-Finnish (FIN) AF: 0.121 AC: 1278 AN: 10600

Middle Eastern (MID) AF: 0.120 AC: 35 AN: 292

European-Non Finnish (NFE) AF: 0.139 AC: 9462 AN: 67952

Other (OTH) AF: 0.167 AC: 352 AN: 2108

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
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs12113442; hg19: chr7-145698191;