15-48036711-T-C

Position:

• chr15-48036711-T-C

Variant summary

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

The ENST00000560900.1(ENSG00000259754):​n.259-12079T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.544 in 151,860 control chromosomes in the GnomAD database, including 22,697 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 0.54 (22697 hom., cov: 31)
• Consequence: ENSG00000259754 ENST00000560900.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

Genes affected

ENSG00000259754 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124900354	XR_001751516.3	n.206-12079T>C		intron_variant
LOC124900354	XR_001751518.3	n.146-12079T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000259754	ENST00000560900.1	n.259-12079T>C		intron_variant		4
ENSG00000259754	ENST00000662551.1	n.252-12079T>C		intron_variant
ENSG00000259754	ENST00000665188.1	n.221-12126T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.544 AC: 82592 AN: 151742 Hom.: 22668 Cov.: 31

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.544 AC: 82679 AN: 151860 Hom.: 22697 Cov.: 31 AF XY: 0.545 AC XY: 40479 AN XY: 74216

Gnomad4 AFR AF: 0.576

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.501

Gnomad4 EAS AF: 0.488

Gnomad4 SAS AF: 0.509

Gnomad4 FIN AF: 0.670

Gnomad4 NFE AF: 0.543

Gnomad4 OTH AF: 0.490

Alfa AF: 0.540 Hom.: 10074

Bravo AF: 0.525

Asia WGS AF: 0.513 AC: 1784 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.22
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1453857; hg19: chr15-48328908;