5-112696978-C-T

Variant names:

• chr5-112696978-C-T
• rs10463643

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 0.274 in 151,926 control chromosomes in the GnomAD database, including 6,769 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 0.27 (6769 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.35 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: 0.275 AC: 41681 AN: 151808 Hom.: 6771 Cov.: 31

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.274 AC: 41697 AN: 151926 Hom.: 6769 Cov.: 31 AF XY: 0.276 AC XY: 20483 AN XY: 74226

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.399

Gnomad4 EAS AF: 0.184

Gnomad4 SAS AF: 0.264

Gnomad4 FIN AF: 0.439

Gnomad4 NFE AF: 0.354

Gnomad4 OTH AF: 0.285

Alfa AF: 0.335 Hom.: 7984

Bravo AF: 0.251

Asia WGS AF: 0.227 AC: 790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.2
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10463643; hg19: chr5-112032675; COSMIC: COSV53481376;