rs4426313

chr15-79510985-C-T

Variant summary

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

The XR_001751629.2(LOC105370919):n.213+6980C>T variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.99

Genes affected

LOC105370919 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370919	XR_001751629.2	n.213+6980C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

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

Gnomad4 AFR AF: 0.643

Gnomad4 AMR AF: 0.691

Gnomad4 ASJ AF: 0.629

Gnomad4 EAS AF: 0.758

Gnomad4 SAS AF: 0.671

Gnomad4 FIN AF: 0.603

Gnomad4 NFE AF: 0.536

Gnomad4 OTH AF: 0.603

Alfa AF: 0.570 Hom.: 4263

Bravo AF: 0.611

Asia WGS AF: 0.714 AC: 2482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.054
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4426313; hg19: chr15-79803327;