rs255982

Variant names:

• chr5-95318169-G-A
• rs255982

Your query was ambiguous. Multiple possible variants found:

• chr5-95318169-G-A
• chr5-95318169-G-C
• chr5-95318169-G-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 0.125 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;