rs4591494

Variant names:

• chr3-7941140-T-C
• rs4591494

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 0.189 in 152,124 control chromosomes in the GnomAD database, including 3,251 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 0.19 (3251 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.531
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28669 AN: 152006 Hom.: 3248 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.189 AC: 28681 AN: 152124 Hom.: 3251 Cov.: 32 AF XY: 0.193 AC XY: 14359 AN XY: 74366

African (AFR) AF: 0.105 AC: 4348 AN: 41510

American (AMR) AF: 0.333 AC: 5087 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 586 AN: 3472

East Asian (EAS) AF: 0.453 AC: 2342 AN: 5170

South Asian (SAS) AF: 0.120 AC: 578 AN: 4824

European-Finnish (FIN) AF: 0.209 AC: 2208 AN: 10582

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.189 AC: 12855 AN: 67996

Other (OTH) AF: 0.238 AC: 503 AN: 2110

Alfa AF: 0.201 Hom.: 14724

Bravo AF: 0.205

Asia WGS AF: 0.271 AC: 942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.2
DANN	Benign	0.86
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs4591494; hg19: chr3-7982827;