rs2496585

chr6-143408310-C-Achr6-143408310-C-T

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 0.208 in 152,118 control chromosomes in the GnomAD database, including 4,366 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 0.21 (4366 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.57

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.311 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: 0.209 AC: 31712 AN: 152000 Hom.: 4370 Cov.: 32

Gnomad AFR AF: 0.0543

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.208 AC: 31699 AN: 152118 Hom.: 4366 Cov.: 32 AF XY: 0.202 AC XY: 15045 AN XY: 74350

Gnomad4 AFR AF: 0.0541

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.278

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.228

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.245

Alfa AF: 0.269 Hom.: 3413

Bravo AF: 0.201

Asia WGS AF: 0.0640 AC: 224 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	9.3
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2496585; hg19: chr6-143729447;