chr1-29590350-C-T

Variant names:

• chr1-29590350-C-T
• rs1932397

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 0.142 in 152,186 control chromosomes in the GnomAD database, including 1,899 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 (1899 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.335 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: 0.142 AC: 21579 AN: 152068 Hom.: 1899 Cov.: 32

Gnomad AFR AF: 0.0499

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.142 AC: 21580 AN: 152186 Hom.: 1899 Cov.: 32 AF XY: 0.143 AC XY: 10624 AN XY: 74410

Gnomad4 AFR AF: 0.0499

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.349

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.157

Alfa AF: 0.166 Hom.: 2871

Bravo AF: 0.141

Asia WGS AF: 0.217 AC: 755 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.8
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1932397; hg19: chr1-30063197;