chr13-95302822-C-T

Variant names:

• chr13-95302822-C-T
• rs868853
• XR_429273.4:n.694+496C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_429273.4(LOC102724149):​n.694+496C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.855 in 152,142 control chromosomes in the GnomAD database, including 56,525 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 0.85 (56525 hom., cov: 32)
• Consequence: LOC102724149 XR_429273.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310

Genes affected

LOC102724149 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.921 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724149	XR_429273.4	n.694+496C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.855 AC: 129929 AN: 152024 Hom.: 56493 Cov.: 32

Gnomad AFR AF: 0.676

Gnomad AMI AF: 0.948

Gnomad AMR AF: 0.910

Gnomad ASJ AF: 0.914

Gnomad EAS AF: 0.866

Gnomad SAS AF: 0.899

Gnomad FIN AF: 0.956

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.927

Gnomad OTH AF: 0.862

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

GnomAD4 genome AF: 0.855 AC: 130010 AN: 152142 Hom.: 56525 Cov.: 32 AF XY: 0.860 AC XY: 63944 AN XY: 74386

Gnomad4 AFR AF: 0.675

Gnomad4 AMR AF: 0.911

Gnomad4 ASJ AF: 0.914

Gnomad4 EAS AF: 0.867

Gnomad4 SAS AF: 0.899

Gnomad4 FIN AF: 0.956

Gnomad4 NFE AF: 0.927

Gnomad4 OTH AF: 0.864

Alfa AF: 0.913 Hom.: 82027

Bravo AF: 0.841

Asia WGS AF: 0.865 AC: 3008 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs868853; hg19: chr13-95955076;