rs1608578

Variant names:

• chr2-129382368-G-A
• rs1608578

Your query was ambiguous. Multiple possible variants found:

• chr2-129382368-G-A
• chr2-129382368-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 0.139 in 151,986 control chromosomes in the GnomAD database, including 3,088 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 0.14 (3088 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) 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: 0.139 AC: 21110 AN: 151868 Hom.: 3072 Cov.: 33

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.0231

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.0436

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0208

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.139 AC: 21155 AN: 151986 Hom.: 3088 Cov.: 33 AF XY: 0.139 AC XY: 10324 AN XY: 74294

Gnomad4 AFR AF: 0.357

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.0231

Gnomad4 EAS AF: 0.248

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.0436

Gnomad4 NFE AF: 0.0208

Gnomad4 OTH AF: 0.124

Alfa AF: 0.0658 Hom.: 232

Bravo AF: 0.156

Asia WGS AF: 0.218 AC: 759 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.058
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1608578; hg19: chr2-130139941;