chr5-52359410-C-T

Variant names:

• chr5-52359410-C-T
• rs1345981

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 0.464 in 151,964 control chromosomes in the GnomAD database, including 16,838 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 0.46 (16838 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.687
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.579 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: 0.464 AC: 70426 AN: 151846 Hom.: 16808 Cov.: 32

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.464 AC: 70517 AN: 151964 Hom.: 16838 Cov.: 32 AF XY: 0.466 AC XY: 34612 AN XY: 74240

African (AFR) AF: 0.566 AC: 23476 AN: 41446

American (AMR) AF: 0.447 AC: 6823 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1186 AN: 3466

East Asian (EAS) AF: 0.592 AC: 3061 AN: 5168

South Asian (SAS) AF: 0.597 AC: 2870 AN: 4806

European-Finnish (FIN) AF: 0.416 AC: 4390 AN: 10562

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.406 AC: 27551 AN: 67938

Other (OTH) AF: 0.411 AC: 867 AN: 2110

Alfa AF: 0.422 Hom.: 41344

Bravo AF: 0.469

Asia WGS AF: 0.614 AC: 2131 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.2
DANN	Benign	0.28
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs1345981; hg19: chr5-51655244;