rs3846728

Variant names:

• chr5-132100524-G-A
• rs3846728

Your query was ambiguous. Multiple possible variants found:

• chr5-132100524-G-A
• chr5-132100524-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 0.337 in 152,068 control chromosomes in the GnomAD database, including 9,784 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 0.34 (9784 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0340

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.44 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: 0.337 AC: 51233 AN: 151950 Hom.: 9786 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.337 AC: 51232 AN: 152068 Hom.: 9784 Cov.: 32 AF XY: 0.328 AC XY: 24366 AN XY: 74332

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.399

Gnomad4 NFE AF: 0.444

Gnomad4 OTH AF: 0.369

Alfa AF: 0.251 Hom.: 644

Bravo AF: 0.330

Asia WGS AF: 0.184 AC: 640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3846728; hg19: chr5-131436217; COSMIC: COSV60199029;