rs1527323

Variant names:

• chr3-74807741-T-G
• rs1527323

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 0.48 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
• Publications: 1 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.470 AC: 19441 AN: 41328

American (AMR) AF: 0.446 AC: 6785 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.536 AC: 1860 AN: 3472

East Asian (EAS) AF: 0.114 AC: 586 AN: 5148

South Asian (SAS) AF: 0.366 AC: 1761 AN: 4812

European-Finnish (FIN) AF: 0.626 AC: 6555 AN: 10468

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.505 AC: 34279 AN: 67894

Other (OTH) AF: 0.445 AC: 937 AN: 2104

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
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs1527323; hg19: chr3-74856892;