11-45023638-T-C

Position:

• chr11-45023638-T-C

Variant summary

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

The ENST00000654627.1(ENSG00000287984):​n.289+15084T>C 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 0.176 in 152,096 control chromosomes in the GnomAD database, including 2,438 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 0.18 (2438 hom., cov: 31)
• Consequence: ENST00000654627.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.480

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376650	XR_931237.3	n.480+15084T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000654627.1	n.289+15084T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26709 AN: 151978 Hom.: 2439 Cov.: 31

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.0864

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.176 AC: 26714 AN: 152096 Hom.: 2438 Cov.: 31 AF XY: 0.172 AC XY: 12762 AN XY: 74358

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.0868

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.168

Alfa AF: 0.180 Hom.: 4845

Bravo AF: 0.178

Asia WGS AF: 0.109 AC: 381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.30
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17093; hg19: chr11-45045189;