rs4426313

Variant names:

• chr15-79510985-C-T
• rs4426313
• XR_001751629.2:n.213+6980C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001751629.2(LOC105370919):​n.213+6980C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.601 in 152,032 control chromosomes in the GnomAD database, including 27,834 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 0.60 (27834 hom., cov: 32)
• Consequence: LOC105370919 XR_001751629.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.99
• Publications: 1 publications found

Genes affected

LOC105370919 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.738 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: 0.601 AC: 91279 AN: 151914 Hom.: 27808 Cov.: 32

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.603

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.601 AC: 91364 AN: 152032 Hom.: 27834 Cov.: 32 AF XY: 0.608 AC XY: 45152 AN XY: 74302

African (AFR) AF: 0.643 AC: 26655 AN: 41454

American (AMR) AF: 0.691 AC: 10562 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.629 AC: 2184 AN: 3470

East Asian (EAS) AF: 0.758 AC: 3916 AN: 5168

South Asian (SAS) AF: 0.671 AC: 3233 AN: 4818

European-Finnish (FIN) AF: 0.603 AC: 6371 AN: 10560

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.536 AC: 36432 AN: 67948

Other (OTH) AF: 0.603 AC: 1274 AN: 2114

Alfa AF: 0.572 Hom.: 4422

Bravo AF: 0.611

Asia WGS AF: 0.714 AC: 2482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.054
DANN	Benign	0.31
PhyloP100		-4.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4426313;

hg19: chr15-79803327;