1-29700254-C-T

Variant names:

• chr1-29700254-C-T
• rs1441834

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.555 AC: 22961 AN: 41400

American (AMR) AF: 0.256 AC: 3911 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 1379 AN: 3470

East Asian (EAS) AF: 0.173 AC: 894 AN: 5160

South Asian (SAS) AF: 0.229 AC: 1104 AN: 4814

European-Finnish (FIN) AF: 0.359 AC: 3774 AN: 10506

Middle Eastern (MID) AF: 0.322 AC: 94 AN: 292

European-Non Finnish (NFE) AF: 0.316 AC: 21479 AN: 67918

Other (OTH) AF: 0.369 AC: 778 AN: 2110

Alfa AF: 0.345 Hom.: 24303

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
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs1441834; hg19: chr1-30173101;