13-48719119-A-G

Variant names:

• chr13-48719119-A-G
• rs12184704

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 0.113 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.222 AC: 9206 AN: 41506

American (AMR) AF: 0.0740 AC: 1130 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0804 AC: 279 AN: 3470

East Asian (EAS) AF: 0.0621 AC: 322 AN: 5182

South Asian (SAS) AF: 0.0824 AC: 397 AN: 4820

European-Finnish (FIN) AF: 0.0725 AC: 769 AN: 10608

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0707 AC: 4805 AN: 67990

Other (OTH) AF: 0.0897 AC: 189 AN: 2108

Alfa AF: 0.0783 Hom.: 306

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
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs12184704; hg19: chr13-49293255;