rs35426

Variant names:

• chr12-115132241-G-A
• rs35426

Your query was ambiguous. Multiple possible variants found:

• chr12-115132241-G-A
• chr12-115132241-G-C
• chr12-115132241-G-T

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 0.692 in 152,090 control chromosomes in the GnomAD database, including 38,174 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 0.69 (38174 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.917 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: 0.691 AC: 105083 AN: 151972 Hom.: 38101 Cov.: 32

Gnomad AFR AF: 0.925

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.692 AC: 105213 AN: 152090 Hom.: 38174 Cov.: 32 AF XY: 0.689 AC XY: 51213 AN XY: 74328

Gnomad4 AFR AF: 0.925

Gnomad4 AMR AF: 0.630

Gnomad4 ASJ AF: 0.667

Gnomad4 EAS AF: 0.792

Gnomad4 SAS AF: 0.637

Gnomad4 FIN AF: 0.569

Gnomad4 NFE AF: 0.584

Gnomad4 OTH AF: 0.675

Alfa AF: 0.603 Hom.: 40795

Bravo AF: 0.704

Asia WGS AF: 0.734 AC: 2549 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.8
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35426; hg19: chr12-115570046;