rs2964186

Positions:

• chr5-58184866-C-T

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 0.413 in 151,846 control chromosomes in the GnomAD database, including 13,601 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 0.41 (13601 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.942

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 (AFR) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

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: 0.413 AC: 62708 AN: 151728 Hom.: 13592 Cov.: 32

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.0278

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.413 AC: 62743 AN: 151846 Hom.: 13601 Cov.: 32 AF XY: 0.404 AC XY: 29971 AN XY: 74218

Gnomad4 AFR AF: 0.459

Gnomad4 AMR AF: 0.361

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.0278

Gnomad4 SAS AF: 0.277

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.442

Gnomad4 OTH AF: 0.407

Alfa AF: 0.434 Hom.: 1784

Bravo AF: 0.417

Asia WGS AF: 0.151 AC: 526 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	1.1
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2964186; hg19: chr5-57480693;