rs3829795

Positions:

• chr1-179576534-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 0.313 in 151,982 control chromosomes in the GnomAD database, including 8,008 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 0.31 (8008 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47635 AN: 151864 Hom.: 8015 Cov.: 32

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.298

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.313 AC: 47643 AN: 151982 Hom.: 8008 Cov.: 32 AF XY: 0.316 AC XY: 23450 AN XY: 74278

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.315

Gnomad4 ASJ AF: 0.351

Gnomad4 EAS AF: 0.501

Gnomad4 SAS AF: 0.343

Gnomad4 FIN AF: 0.372

Gnomad4 NFE AF: 0.355

Gnomad4 OTH AF: 0.318

Alfa AF: 0.343 Hom.: 8490

Bravo AF: 0.304

Asia WGS AF: 0.372 AC: 1291 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3829795; hg19: chr1-179545669;