rs1561806

chr15-88312953-C-T

Variant summary

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

The XR_932589.2(LOC105370958):n.1057-5851C>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 0.58 in 152,098 control chromosomes in the GnomAD database, including 26,661 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 0.58 (26661 hom., cov: 32)
• Consequence: LOC105370958 XR_932589.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.641

Genes affected

LOC105370958 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370958	XR_932589.2	n.1057-5851C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.580 AC: 88134 AN: 151980 Hom.: 26596 Cov.: 32

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.642

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.767

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.580 AC: 88265 AN: 152098 Hom.: 26661 Cov.: 32 AF XY: 0.582 AC XY: 43263 AN XY: 74348

Gnomad4 AFR AF: 0.730

Gnomad4 AMR AF: 0.643

Gnomad4 ASJ AF: 0.502

Gnomad4 EAS AF: 0.767

Gnomad4 SAS AF: 0.601

Gnomad4 FIN AF: 0.470

Gnomad4 NFE AF: 0.484

Gnomad4 OTH AF: 0.569

Alfa AF: 0.508 Hom.: 26610

Bravo AF: 0.600

Asia WGS AF: 0.706 AC: 2457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.24
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1561806; hg19: chr15-88856184;