rs186682

chr5-57138557-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

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 0.023 (11 hom., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.351

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.023 (758/33028) while in subpopulation SAS AF= 0.0369 (35/948). AF 95% confidence interval is 0.0273. There are 11 homozygotes in gnomad4. There are 379 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 11 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0230 AC: 758 AN: 32986 Hom.: 11 Cov.: 0

Gnomad AFR AF: 0.0302

Gnomad AMI AF: 0.00446

Gnomad AMR AF: 0.0213

Gnomad ASJ AF: 0.0313

Gnomad EAS AF: 0.00931

Gnomad SAS AF: 0.0371

Gnomad FIN AF: 0.0329

Gnomad MID AF: 0.0536

Gnomad NFE AF: 0.0192

Gnomad OTH AF: 0.0332

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

GnomAD4 genome AF: 0.0230 AC: 758 AN: 33028 Hom.: 11 Cov.: 0 AF XY: 0.0240 AC XY: 379 AN XY: 15788

Gnomad4 AFR AF: 0.0301

Gnomad4 AMR AF: 0.0213

Gnomad4 ASJ AF: 0.0313

Gnomad4 EAS AF: 0.00934

Gnomad4 SAS AF: 0.0369

Gnomad4 FIN AF: 0.0329

Gnomad4 NFE AF: 0.0192

Gnomad4 OTH AF: 0.0318

Alfa AF: 0.291 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.57
Dann	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs186682; hg19: chr5-56434384; COSMIC: COSV51295569;