rs3734168

Variant names:

• chr5-138350001-C-A
• rs3734168

Your query was ambiguous. Multiple possible variants found:

• chr5-138350001-C-A
• chr5-138350001-C-G

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 0.251 in 152,230 control chromosomes in the GnomAD database, including 5,527 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 (5527 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.112

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.545 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: 0.251 AC: 38254 AN: 152110 Hom.: 5520 Cov.: 33

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.251 AC: 38280 AN: 152230 Hom.: 5527 Cov.: 33 AF XY: 0.255 AC XY: 19004 AN XY: 74438

Gnomad4 AFR AF: 0.350

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.229

Gnomad4 EAS AF: 0.562

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.259

Alfa AF: 0.130 Hom.: 262

Bravo AF: 0.265

Asia WGS AF: 0.350 AC: 1219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	14
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3734168; hg19: chr5-137685690; COSMIC: COSV53511104;