3-185635347-G-A

Variant names:

• chr3-185635347-G-A
• rs4575929

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 0.364 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
• Publications: 11 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.388 AC: 16060 AN: 41408

American (AMR) AF: 0.371 AC: 5661 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1418 AN: 3470

East Asian (EAS) AF: 0.303 AC: 1567 AN: 5166

South Asian (SAS) AF: 0.553 AC: 2663 AN: 4818

European-Finnish (FIN) AF: 0.314 AC: 3303 AN: 10534

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23567 AN: 67982

Other (OTH) AF: 0.335 AC: 708 AN: 2116

Alfa AF: 0.343 Hom.: 3430

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
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs4575929; hg19: chr3-185353135;