rs4365667

Variant names:

• chr3-165919741-C-A
• rs4365667

Your query was ambiguous. Multiple possible variants found:

• chr3-165919741-C-A
• chr3-165919741-C-T

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 0.344 in 151,954 control chromosomes in the GnomAD database, including 10,300 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 0.34 (10300 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.681
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.543 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: 0.344 AC: 52259 AN: 151836 Hom.: 10279 Cov.: 32

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.344 AC: 52315 AN: 151954 Hom.: 10300 Cov.: 32 AF XY: 0.337 AC XY: 25008 AN XY: 74284

African (AFR) AF: 0.549 AC: 22735 AN: 41408

American (AMR) AF: 0.279 AC: 4259 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1006 AN: 3472

East Asian (EAS) AF: 0.142 AC: 733 AN: 5152

South Asian (SAS) AF: 0.176 AC: 847 AN: 4812

European-Finnish (FIN) AF: 0.261 AC: 2759 AN: 10564

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 19002 AN: 67968

Other (OTH) AF: 0.322 AC: 680 AN: 2114

Alfa AF: 0.297 Hom.: 23231

Bravo AF: 0.355

Asia WGS AF: 0.207 AC: 723 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.30
DANN	Benign	0.26
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs4365667; hg19: chr3-165637529;