rs4591494

Variant names:

• chr3-7941140-T-C
• rs4591494

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 0.189 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.189 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

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.333

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.453

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.238

Alfa AF: 0.204 Hom.: 7519

Bravo AF: 0.205

Asia WGS AF: 0.271 AC: 942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4591494; hg19: chr3-7982827;