chr3-5847593-T-A

Variant names:

• chr3-5847593-T-A
• rs748192

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 0.147 in 152,094 control chromosomes in the GnomAD database, including 1,853 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 0.15 (1853 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.218 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: 0.147 AC: 22319 AN: 151978 Hom.: 1854 Cov.: 31

Gnomad AFR AF: 0.0905

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.147 AC: 22329 AN: 152094 Hom.: 1853 Cov.: 31 AF XY: 0.148 AC XY: 11024 AN XY: 74354

Gnomad4 AFR AF: 0.0904

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.175

Alfa AF: 0.149 Hom.: 187

Bravo AF: 0.149

Asia WGS AF: 0.113 AC: 392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.90
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs748192; hg19: chr3-5889280;