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. The variant received -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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.769 AC: 31880 AN: 41468

American (AMR) AF: 0.498 AC: 7618 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1117 AN: 3470

East Asian (EAS) AF: 0.449 AC: 2306 AN: 5138

South Asian (SAS) AF: 0.321 AC: 1548 AN: 4816

European-Finnish (FIN) AF: 0.339 AC: 3587 AN: 10580

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.323 AC: 21934 AN: 67970

Other (OTH) AF: 0.475 AC: 1004 AN: 2112

Alfa AF: 0.365 Hom.: 18386

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
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs346005; hg19: chr4-53454738;