15-40964568-C-T

Variant names:

• chr15-40964568-C-T
• rs1869907
• XR_001751507.3:n.1154-71C>T

Variant summary

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

The XR_932166.4(LOC105370789):​n.1227-71C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 151,594 control chromosomes in the GnomAD database, including 19,807 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 0.50 (19807 hom., cov: 29)
• Consequence: LOC105370789 XR_932166.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.187

Genes affected

LOC105370789 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370789	XR_001751507.3	n.1154-71C>T		intron_variant	Intron 3 of 3
LOC105370789	XR_007064601.1	n.1227-71C>T		intron_variant	Intron 2 of 3
LOC105370789	XR_932166.4	n.1227-71C>T		intron_variant	Intron 2 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76226 AN: 151476 Hom.: 19802 Cov.: 29

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.684

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.503 AC: 76250 AN: 151594 Hom.: 19807 Cov.: 29 AF XY: 0.509 AC XY: 37661 AN XY: 74056

Gnomad4 AFR AF: 0.371

Gnomad4 AMR AF: 0.558

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.684

Gnomad4 SAS AF: 0.472

Gnomad4 FIN AF: 0.649

Gnomad4 NFE AF: 0.536

Gnomad4 OTH AF: 0.502

Alfa AF: 0.522 Hom.: 20284

Bravo AF: 0.494

Asia WGS AF: 0.546 AC: 1903 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.85
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1869907; hg19: chr15-41256766;