rs2496585

Variant names:

• chr6-143408310-C-A
• rs2496585

Your query was ambiguous. Multiple possible variants found:

• chr6-143408310-C-A
• chr6-143408310-C-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0541 AC: 2249 AN: 41544

American (AMR) AF: 0.211 AC: 3228 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 963 AN: 3462

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5184

South Asian (SAS) AF: 0.110 AC: 529 AN: 4824

European-Finnish (FIN) AF: 0.228 AC: 2411 AN: 10566

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21395 AN: 67942

Other (OTH) AF: 0.245 AC: 519 AN: 2116

Alfa AF: 0.280 Hom.: 5183

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
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs2496585; hg19: chr6-143729447;