rs1324329

Positions:

• chr1-193453636-A-G

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 0.147 in 151,902 control chromosomes in the GnomAD database, including 2,166 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 0.15 (2166 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.165

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.341 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: 0.147 AC: 22313 AN: 151784 Hom.: 2150 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0907

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0858

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.147 AC: 22367 AN: 151902 Hom.: 2166 Cov.: 32 AF XY: 0.148 AC XY: 11016 AN XY: 74242

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.206

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.354

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.0907

Gnomad4 NFE AF: 0.0858

Gnomad4 OTH AF: 0.144

Alfa AF: 0.130 Hom.: 358

Bravo AF: 0.162

Asia WGS AF: 0.214 AC: 745 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.1
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1324329; hg19: chr1-193422766; COSMIC: COSV60005630;