rs17036101

Variant names:

• chr3-12236345-G-A
• rs17036101

Your query was ambiguous. Multiple possible variants found:

• chr3-12236345-G-A
• chr3-12236345-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 0.0486 in 152,032 control chromosomes in the GnomAD database, including 213 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 0.049 (213 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.320

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0622 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: 0.0486 AC: 7384 AN: 151914 Hom.: 211 Cov.: 32

Gnomad AFR AF: 0.0261

Gnomad AMI AF: 0.00441

Gnomad AMR AF: 0.0280

Gnomad ASJ AF: 0.0325

Gnomad EAS AF: 0.0321

Gnomad SAS AF: 0.0496

Gnomad FIN AF: 0.0901

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0638

Gnomad OTH AF: 0.0279

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

GnomAD4 genome AF: 0.0486 AC: 7390 AN: 152032 Hom.: 213 Cov.: 32 AF XY: 0.0495 AC XY: 3677 AN XY: 74290

Gnomad4 AFR AF: 0.0262

Gnomad4 AMR AF: 0.0279

Gnomad4 ASJ AF: 0.0325

Gnomad4 EAS AF: 0.0320

Gnomad4 SAS AF: 0.0498

Gnomad4 FIN AF: 0.0901

Gnomad4 NFE AF: 0.0638

Gnomad4 OTH AF: 0.0276

Alfa AF: 0.0542 Hom.: 289

Bravo AF: 0.0422

Asia WGS AF: 0.0300 AC: 104 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.80
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17036101; hg19: chr3-12277845;