13-48646057-G-C

Variant names:

• chr13-48646057-G-C
• rs2406939

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 0.497 in 151,986 control chromosomes in the GnomAD database, including 21,473 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 0.50 (21473 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.706

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.788 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: 0.496 AC: 75363 AN: 151868 Hom.: 21414 Cov.: 31

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.497 AC: 75483 AN: 151986 Hom.: 21473 Cov.: 31 AF XY: 0.496 AC XY: 36831 AN XY: 74312

Gnomad4 AFR AF: 0.795

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.429

Gnomad4 EAS AF: 0.454

Gnomad4 SAS AF: 0.430

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.376

Gnomad4 OTH AF: 0.448

Alfa AF: 0.307 Hom.: 816

Bravo AF: 0.506

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.77
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2406939; hg19: chr13-49220193;