5-32670694-C-T

Variant names:

• chr5-32670694-C-T
• rs1862523

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 0.608 in 152,034 control chromosomes in the GnomAD database, including 28,784 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 0.61 (28784 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.683 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: 0.608 AC: 92398 AN: 151916 Hom.: 28775 Cov.: 32

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.608 AC: 92446 AN: 152034 Hom.: 28784 Cov.: 32 AF XY: 0.605 AC XY: 44973 AN XY: 74296

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.571

Gnomad4 ASJ AF: 0.671

Gnomad4 EAS AF: 0.423

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.671

Gnomad4 NFE AF: 0.688

Gnomad4 OTH AF: 0.632

Alfa AF: 0.671 Hom.: 47563

Bravo AF: 0.594

Asia WGS AF: 0.486 AC: 1693 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.3
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1862523; hg19: chr5-32670800;