15-26142332-T-C

Variant names:

• chr15-26142332-T-C
• rs4906863
• XR_932004.3:n.105+562A>G

Variant summary

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

The XR_932004.3(LOC105370739):​n.105+562A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 109,338 control chromosomes in the GnomAD database, including 821 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 0.12 (821 hom., cov: 30)
• Consequence: LOC105370739 XR_932004.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.60

Genes affected

LOC105370739 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370739	XR_932004.3	n.105+562A>G		intron_variant	Intron 1 of 4
LOC105370739	XR_932005.3	n.105+562A>G		intron_variant	Intron 1 of 5

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.119 AC: 12987 AN: 109314 Hom.: 820 Cov.: 30

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.0394

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.0161

Gnomad SAS AF: 0.0686

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.0850

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.119 AC: 12992 AN: 109338 Hom.: 821 Cov.: 30 AF XY: 0.121 AC XY: 6358 AN XY: 52660

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.0162

Gnomad4 SAS AF: 0.0678

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.121

Alfa AF: 0.0319 Hom.: 20

Bravo AF: 0.126

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4906863; hg19: chr15-26387479;