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. The variant received -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
• Publications: 43 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0262 AC: 1088 AN: 41458

American (AMR) AF: 0.0279 AC: 427 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0325 AC: 113 AN: 3472

East Asian (EAS) AF: 0.0320 AC: 166 AN: 5188

South Asian (SAS) AF: 0.0498 AC: 240 AN: 4816

European-Finnish (FIN) AF: 0.0901 AC: 948 AN: 10520

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0638 AC: 4335 AN: 67990

Other (OTH) AF: 0.0276 AC: 58 AN: 2102

Alfa AF: 0.0559 Hom.: 814

Bravo AF: 0.0422

Asia WGS AF: 0.0300 AC: 104 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.80
DANN	Benign	0.34
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs17036101; hg19: chr3-12277845;