rs1527323

Positions:

• chr3-74807741-T-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 0.48 in 151,660 control chromosomes in the GnomAD database, including 18,171 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 0.48 (18171 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.121

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.5 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: 0.480 AC: 72787 AN: 151542 Hom.: 18159 Cov.: 31

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.480 AC: 72840 AN: 151660 Hom.: 18171 Cov.: 31 AF XY: 0.481 AC XY: 35675 AN XY: 74120

Gnomad4 AFR AF: 0.470

Gnomad4 AMR AF: 0.446

Gnomad4 ASJ AF: 0.536

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.626

Gnomad4 NFE AF: 0.505

Gnomad4 OTH AF: 0.445

Alfa AF: 0.502 Hom.: 2405

Bravo AF: 0.467

Asia WGS AF: 0.265 AC: 924 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	6.7
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1527323; hg19: chr3-74856892;