rs4575929

chr3-185635347-G-Achr3-185635347-G-Cchr3-185635347-G-T

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 0.364 in 151,968 control chromosomes in the GnomAD database, including 10,197 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 0.36 (10197 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.535 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: 0.364 AC: 55267 AN: 151846 Hom.: 10183 Cov.: 32

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.364 AC: 55331 AN: 151968 Hom.: 10197 Cov.: 32 AF XY: 0.367 AC XY: 27287 AN XY: 74266

Gnomad4 AFR AF: 0.388

Gnomad4 AMR AF: 0.371

Gnomad4 ASJ AF: 0.409

Gnomad4 EAS AF: 0.303

Gnomad4 SAS AF: 0.553

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.335

Alfa AF: 0.343 Hom.: 2691

Bravo AF: 0.358

Asia WGS AF: 0.413 AC: 1435 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.1
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4575929; hg19: chr3-185353135;