15-48009867-G-A

Position:

• chr15-48009867-G-A

Variant summary

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

The ENST00000662551.1(ENSG00000259754):​n.251+17096G>A 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 0.305 in 152,108 control chromosomes in the GnomAD database, including 9,162 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 0.30 (9162 hom., cov: 32)
• Consequence: ENST00000662551.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.76

Genes affected

(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 (NFE) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124900354	XR_001751516.3	n.205+17096G>A		intron_variant, non_coding_transcript_variant
LOC124900354	XR_001751518.3	n.145+17096G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000662551.1	n.251+17096G>A		intron_variant, non_coding_transcript_variant
	ENST00000560900.1	n.258+17096G>A		intron_variant, non_coding_transcript_variant		4
	ENST00000665188.1	n.220+11712G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46374 AN: 151990 Hom.: 9163 Cov.: 32

Gnomad AFR AF: 0.0887

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.0241

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.305 AC: 46364 AN: 152108 Hom.: 9162 Cov.: 32 AF XY: 0.306 AC XY: 22755 AN XY: 74354

Gnomad4 AFR AF: 0.0885

Gnomad4 AMR AF: 0.245

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.0239

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.501

Gnomad4 NFE AF: 0.435

Gnomad4 OTH AF: 0.292

Alfa AF: 0.388 Hom.: 12198

Bravo AF: 0.272

Asia WGS AF: 0.152 AC: 531 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	12
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17423970; hg19: chr15-48302064;