13-48719119-A-G

Position:

• chr13-48719119-A-G

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 0.113 in 152,162 control chromosomes in the GnomAD database, including 1,326 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 0.11 (1326 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.574

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17160 AN: 152044 Hom.: 1319 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0742

Gnomad ASJ AF: 0.0804

Gnomad EAS AF: 0.0622

Gnomad SAS AF: 0.0821

Gnomad FIN AF: 0.0725

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0707

Gnomad OTH AF: 0.0906

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

GnomAD4 genome AF: 0.113 AC: 17188 AN: 152162 Hom.: 1326 Cov.: 32 AF XY: 0.112 AC XY: 8305 AN XY: 74408

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.0740

Gnomad4 ASJ AF: 0.0804

Gnomad4 EAS AF: 0.0621

Gnomad4 SAS AF: 0.0824

Gnomad4 FIN AF: 0.0725

Gnomad4 NFE AF: 0.0707

Gnomad4 OTH AF: 0.0897

Alfa AF: 0.0739 Hom.: 229

Bravo AF: 0.116

Asia WGS AF: 0.0690 AC: 242 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.2
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12184704; hg19: chr13-49293255;