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. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.350 AC: 14541 AN: 41500

American (AMR) AF: 0.255 AC: 3904 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 795 AN: 3472

East Asian (EAS) AF: 0.562 AC: 2917 AN: 5186

South Asian (SAS) AF: 0.177 AC: 853 AN: 4826

European-Finnish (FIN) AF: 0.205 AC: 2172 AN: 10610

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.179 AC: 12177 AN: 68024

Other (OTH) AF: 0.259 AC: 547 AN: 2114

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
PhyloP100		0.11

Splicing

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

Other links and lift over

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