rs1122080

Variant names:

• chr5-158588895-G-A
• rs1122080

Your query was ambiguous. Multiple possible variants found:

• chr5-158588895-G-A
• chr5-158588895-G-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.212 in 152,154 control chromosomes in the GnomAD database, including 3,670 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 0.21 (3670 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.29

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.25).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.352 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: 0.212 AC: 32164 AN: 152036 Hom.: 3663 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.212 AC: 32194 AN: 152154 Hom.: 3670 Cov.: 32 AF XY: 0.211 AC XY: 15711 AN XY: 74378

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.153

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.216

Alfa AF: 0.190 Hom.: 355

Bravo AF: 0.222

Asia WGS AF: 0.341 AC: 1186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
CADD	Benign	18
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1122080; hg19: chr5-158015903;