rs1162374

Variant names:

• chr12-88457766-G-A
• rs1162374

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 0.255 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.572 AC: 23656 AN: 41386

American (AMR) AF: 0.152 AC: 2315 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0835 AC: 290 AN: 3472

East Asian (EAS) AF: 0.186 AC: 961 AN: 5162

South Asian (SAS) AF: 0.250 AC: 1202 AN: 4816

European-Finnish (FIN) AF: 0.110 AC: 1146 AN: 10462

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8576 AN: 67962

Other (OTH) AF: 0.212 AC: 447 AN: 2104

Alfa AF: 0.209 Hom.: 1304

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
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs1162374; hg19: chr12-88851543;