rs2196302

Variant names:

• chr3-5763409-G-A
• rs2196302

Your query was ambiguous. Multiple possible variants found:

• chr3-5763409-G-A
• chr3-5763409-G-C
• chr3-5763409-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 0.365 in 152,008 control chromosomes in the GnomAD database, including 12,114 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 0.37 (12114 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.49 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: 0.366 AC: 55558 AN: 151890 Hom.: 12116 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.365 AC: 55556 AN: 152008 Hom.: 12114 Cov.: 32 AF XY: 0.365 AC XY: 27146 AN XY: 74302

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.336

Gnomad4 SAS AF: 0.328

Gnomad4 FIN AF: 0.565

Gnomad4 NFE AF: 0.495

Gnomad4 OTH AF: 0.346

Alfa AF: 0.448 Hom.: 9469

Bravo AF: 0.334

Asia WGS AF: 0.286 AC: 995 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.92
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2196302; hg19: chr3-5805096;