rs2859338

Variant names:

• chr6-12298751-G-A
• rs2859338

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 0.298 in 152,144 control chromosomes in the GnomAD database, including 8,685 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 0.30 (8685 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.32

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.425 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: 0.298 AC: 45318 AN: 152026 Hom.: 8688 Cov.: 33

Gnomad AFR AF: 0.0771

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.0385

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.298 AC: 45308 AN: 152144 Hom.: 8685 Cov.: 33 AF XY: 0.295 AC XY: 21933 AN XY: 74362

Gnomad4 AFR AF: 0.0769

Gnomad4 AMR AF: 0.312

Gnomad4 ASJ AF: 0.377

Gnomad4 EAS AF: 0.0386

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.418

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.317

Alfa AF: 0.397 Hom.: 17505

Bravo AF: 0.279

Asia WGS AF: 0.126 AC: 439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	9.9
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2859338; hg19: chr6-12298984;