rs346005

Variant names:

• chr4-52588572-A-C
• rs346005

Your query was ambiguous. Multiple possible variants found:

• chr4-52588572-A-C
• chr4-52588572-A-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 0.47 in 152,044 control chromosomes in the GnomAD database, including 19,623 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 0.47 (19623 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.876

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 (AFR) allele frequency at 95% confidence interval = 0.762 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: 0.469 AC: 71274 AN: 151926 Hom.: 19558 Cov.: 32

Gnomad AFR AF: 0.768

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.470 AC: 71407 AN: 152044 Hom.: 19623 Cov.: 32 AF XY: 0.468 AC XY: 34754 AN XY: 74284

Gnomad4 AFR AF: 0.769

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.449

Gnomad4 SAS AF: 0.321

Gnomad4 FIN AF: 0.339

Gnomad4 NFE AF: 0.323

Gnomad4 OTH AF: 0.475

Alfa AF: 0.347 Hom.: 12801

Bravo AF: 0.500

Asia WGS AF: 0.441 AC: 1532 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs346005; hg19: chr4-53454738;