13-48646057-G-C

Variant names:

• chr13-48646057-G-C
• rs2406939

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 0.497 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.795 AC: 32981 AN: 41464

American (AMR) AF: 0.349 AC: 5330 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.429 AC: 1487 AN: 3466

East Asian (EAS) AF: 0.454 AC: 2346 AN: 5168

South Asian (SAS) AF: 0.430 AC: 2068 AN: 4804

European-Finnish (FIN) AF: 0.409 AC: 4316 AN: 10564

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

European-Non Finnish (NFE) AF: 0.376 AC: 25556 AN: 67932

Other (OTH) AF: 0.448 AC: 944 AN: 2106

Alfa AF: 0.307 Hom.: 816

Bravo AF: 0.506

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.77
DANN	Benign	0.56
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs2406939; hg19: chr13-49220193;