rs365188

Variant names:

• chr5-102741554-T-C
• rs365188

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 0.361 in 151,930 control chromosomes in the GnomAD database, including 10,392 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 0.36 (10392 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.406 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: 0.361 AC: 54792 AN: 151812 Hom.: 10392 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.361 AC: 54813 AN: 151930 Hom.: 10392 Cov.: 32 AF XY: 0.364 AC XY: 26995 AN XY: 74258

Gnomad4 AFR AF: 0.252

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.363

Gnomad4 SAS AF: 0.413

Gnomad4 FIN AF: 0.453

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.332

Alfa AF: 0.388 Hom.: 1796

Bravo AF: 0.351

Asia WGS AF: 0.369 AC: 1276 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs365188; hg19: chr5-102077258; COSMIC: COSV60174920;