5-92818872-T-C

Variant names:

• chr5-92818872-T-C
• rs17668565

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 0.459 in 152,048 control chromosomes in the GnomAD database, including 16,790 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 (16790 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.40

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.532 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: 0.459 AC: 69760 AN: 151930 Hom.: 16790 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.397

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.459 AC: 69799 AN: 152048 Hom.: 16790 Cov.: 32 AF XY: 0.458 AC XY: 34059 AN XY: 74298

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.444

Gnomad4 ASJ AF: 0.514

Gnomad4 EAS AF: 0.253

Gnomad4 SAS AF: 0.410

Gnomad4 FIN AF: 0.576

Gnomad4 NFE AF: 0.536

Gnomad4 OTH AF: 0.468

Alfa AF: 0.513 Hom.: 35553

Bravo AF: 0.444

Asia WGS AF: 0.344 AC: 1196 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	8.6
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17668565; hg19: chr5-92154579; COSMIC: COSV60167821;