rs314413

Variant names:

• chr13-89132815-A-G
• rs314413

Your query was ambiguous. Multiple possible variants found:

• chr13-89132815-A-G
• chr13-89132815-A-T

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 0.886 in 152,042 control chromosomes in the GnomAD database, including 60,890 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 0.89 (60890 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.978 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: 0.886 AC: 134556 AN: 151924 Hom.: 60862 Cov.: 32

Gnomad AFR AF: 0.702

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.949

Gnomad ASJ AF: 0.905

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.893

Gnomad FIN AF: 0.923

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.985

Gnomad OTH AF: 0.901

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

GnomAD4 genome AF: 0.886 AC: 134636 AN: 152042 Hom.: 60890 Cov.: 32 AF XY: 0.883 AC XY: 65608 AN XY: 74314

African (AFR) AF: 0.702 AC: 29080 AN: 41450

American (AMR) AF: 0.950 AC: 14497 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.905 AC: 3142 AN: 3472

East Asian (EAS) AF: 0.740 AC: 3811 AN: 5148

South Asian (SAS) AF: 0.892 AC: 4302 AN: 4824

European-Finnish (FIN) AF: 0.923 AC: 9756 AN: 10566

Middle Eastern (MID) AF: 0.945 AC: 276 AN: 292

European-Non Finnish (NFE) AF: 0.985 AC: 66957 AN: 67996

Other (OTH) AF: 0.900 AC: 1903 AN: 2114

Alfa AF: 0.923 Hom.: 8000

Bravo AF: 0.880

Asia WGS AF: 0.833 AC: 2881 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.9
DANN	Benign	0.87
PhyloP100		-0.051

Splicing

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

Other links and lift over

dbSNP: rs314413; hg19: chr13-89785069;