rs1586340

Variant names:

• chr4-91936104-T-C
• rs1586340

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 0.187 in 152,058 control chromosomes in the GnomAD database, including 3,448 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 (3448 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.341 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: 0.187 AC: 28357 AN: 151940 Hom.: 3434 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.0714

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.187 AC: 28418 AN: 152058 Hom.: 3448 Cov.: 32 AF XY: 0.184 AC XY: 13691 AN XY: 74350

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.156

Gnomad4 SAS AF: 0.185

Gnomad4 FIN AF: 0.0714

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.197

Alfa AF: 0.141 Hom.: 1098

Bravo AF: 0.197

Asia WGS AF: 0.202 AC: 707 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1586340; hg19: chr4-92857255;