rs1162374

Variant names:

• chr12-88457766-G-A
• rs1162374

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 0.255 in 151,832 control chromosomes in the GnomAD database, including 7,923 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 0.25 (7923 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.565 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: 0.254 AC: 38600 AN: 151712 Hom.: 7877 Cov.: 31

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.0835

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.255 AC: 38694 AN: 151832 Hom.: 7923 Cov.: 31 AF XY: 0.250 AC XY: 18552 AN XY: 74214

Gnomad4 AFR AF: 0.572

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.0835

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.212

Alfa AF: 0.198 Hom.: 1085

Bravo AF: 0.269

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.4
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1162374; hg19: chr12-88851543;