5-56252970-T-C

Variant names:

• chr5-56252970-T-C
• rs32498

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 0.46 in 152,014 control chromosomes in the GnomAD database, including 19,452 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 (19452 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.661

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.768 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: 0.460 AC: 69803 AN: 151898 Hom.: 19413 Cov.: 32

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.460 AC: 69892 AN: 152014 Hom.: 19452 Cov.: 32 AF XY: 0.465 AC XY: 34537 AN XY: 74314

Gnomad4 AFR AF: 0.775

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.673

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.289

Gnomad4 OTH AF: 0.429

Alfa AF: 0.318 Hom.: 16635

Bravo AF: 0.472

Asia WGS AF: 0.551 AC: 1917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.80
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs32498; hg19: chr5-55548797; COSMIC: COSV60133736;