rs1608578

Positions:

• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;