15-45736425-A-T

Position:

• chr15-45736425-A-T

Variant summary

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

The NR_135680.1(LOC105370802):​n.95+31136A>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 0.0939 in 152,188 control chromosomes in the GnomAD database, including 1,063 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 0.094 (1063 hom., cov: 32)
• Consequence: LOC105370802 NR_135680.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370802	NR_135680.1	n.95+31136A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000559600.1	n.95+31136A>T		intron_variant, non_coding_transcript_variant		3
	ENST00000560705.1	n.317+29655A>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0940 AC: 14287 AN: 152070 Hom.: 1065 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.0457

Gnomad ASJ AF: 0.0649

Gnomad EAS AF: 0.0177

Gnomad SAS AF: 0.0209

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0525

Gnomad OTH AF: 0.0817

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

GnomAD4 genome AF: 0.0939 AC: 14296 AN: 152188 Hom.: 1063 Cov.: 32 AF XY: 0.0941 AC XY: 7006 AN XY: 74422

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.0457

Gnomad4 ASJ AF: 0.0649

Gnomad4 EAS AF: 0.0178

Gnomad4 SAS AF: 0.0205

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.0524

Gnomad4 OTH AF: 0.0808

Alfa AF: 0.0176 Hom.: 11

Bravo AF: 0.0944

Asia WGS AF: 0.0340 AC: 120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16947598; hg19: chr15-46028623;