rs2502389

Variant names:

• chr6-113146970-C-T
• rs2502389

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 0.457 in 152,024 control chromosomes in the GnomAD database, including 16,471 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 0.46 (16471 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.886

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.575 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: 0.457 AC: 69425 AN: 151906 Hom.: 16452 Cov.: 32

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.457 AC: 69497 AN: 152024 Hom.: 16471 Cov.: 32 AF XY: 0.459 AC XY: 34103 AN XY: 74292

Gnomad4 AFR AF: 0.581

Gnomad4 AMR AF: 0.422

Gnomad4 ASJ AF: 0.456

Gnomad4 EAS AF: 0.483

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.454

Alfa AF: 0.405 Hom.: 5970

Bravo AF: 0.463

Asia WGS AF: 0.398 AC: 1384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.048
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2502389; hg19: chr6-113468172; COSMIC: COSV68646779;