rs1325507

Positions:

• chr1-152646788-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 0.172 in 152,088 control chromosomes in the GnomAD database, including 3,137 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 0.17 (3137 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.434

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.326 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: 0.172 AC: 26066 AN: 151970 Hom.: 3122 Cov.: 32

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.0834

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0826

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.172 AC: 26110 AN: 152088 Hom.: 3137 Cov.: 32 AF XY: 0.174 AC XY: 12967 AN XY: 74362

Gnomad4 AFR AF: 0.331

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.0834

Gnomad4 EAS AF: 0.292

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.0826

Gnomad4 OTH AF: 0.161

Alfa AF: 0.107 Hom.: 678

Bravo AF: 0.177

Asia WGS AF: 0.244 AC: 848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.1
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1325507; hg19: chr1-152619264;