rs1441834

Positions:

• chr1-29700254-C-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 0.373 in 151,854 control chromosomes in the GnomAD database, including 11,674 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 0.37 (11674 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.923

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.549 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: 0.373 AC: 56644 AN: 151736 Hom.: 11654 Cov.: 32

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.373 AC: 56708 AN: 151854 Hom.: 11674 Cov.: 32 AF XY: 0.370 AC XY: 27463 AN XY: 74212

Gnomad4 AFR AF: 0.555

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.173

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.369

Alfa AF: 0.331 Hom.: 12251

Bravo AF: 0.378

Asia WGS AF: 0.220 AC: 769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.87
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1441834; hg19: chr1-30173101;