rs6586395

Positions:

• chr1-234513073-A-C

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 0.253 in 151,822 control chromosomes in the GnomAD database, including 10,879 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 0.25 (10879 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.535

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 (AFR) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38274 AN: 151704 Hom.: 10829 Cov.: 30

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.0916

Gnomad EAS AF: 0.00716

Gnomad SAS AF: 0.0785

Gnomad FIN AF: 0.0385

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0795

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.253 AC: 38380 AN: 151822 Hom.: 10879 Cov.: 30 AF XY: 0.245 AC XY: 18210 AN XY: 74248

Gnomad4 AFR AF: 0.704

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.0916

Gnomad4 EAS AF: 0.00737

Gnomad4 SAS AF: 0.0775

Gnomad4 FIN AF: 0.0385

Gnomad4 NFE AF: 0.0795

Gnomad4 OTH AF: 0.206

Alfa AF: 0.112 Hom.: 3325

Bravo AF: 0.282

Asia WGS AF: 0.106 AC: 368 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	0.24
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6586395; hg19: chr1-234648819;