rs255982

chr5-95318169-G-A

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 0.125 in 152,086 control chromosomes in the GnomAD database, including 1,395 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 0.12 (1395 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.471

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.155 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: 0.125 AC: 19006 AN: 151968 Hom.: 1394 Cov.: 31

Gnomad AFR AF: 0.0493

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.0411

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.125 AC: 19005 AN: 152086 Hom.: 1395 Cov.: 31 AF XY: 0.128 AC XY: 9511 AN XY: 74346

Gnomad4 AFR AF: 0.0492

Gnomad4 AMR AF: 0.150

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.0412

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.132

Alfa AF: 0.131 Hom.: 404

Bravo AF: 0.115

Asia WGS AF: 0.0770 AC: 265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	5.9
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs255982; hg19: chr5-94653873;