11-45030276-C-T

Variant names:

• chr11-45030276-C-T
• rs754970
• ENST00000654627.1:n.290-11261C>T

Variant summary

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

The ENST00000654627.1(ENSG00000287984):​n.290-11261C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.599 in 152,066 control chromosomes in the GnomAD database, including 27,490 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 0.60 (27490 hom., cov: 32)
• Consequence: ENSG00000287984 ENST00000654627.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.177

Genes affected

ENSG00000287984 (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 (EAS) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376650	XR_931237.3	n.481-11261C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287984	ENST00000654627.1	n.290-11261C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.599 AC: 90982 AN: 151948 Hom.: 27472 Cov.: 32

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.817

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.599 AC: 91049 AN: 152066 Hom.: 27490 Cov.: 32 AF XY: 0.602 AC XY: 44756 AN XY: 74340

Gnomad4 AFR AF: 0.555

Gnomad4 AMR AF: 0.571

Gnomad4 ASJ AF: 0.608

Gnomad4 EAS AF: 0.816

Gnomad4 SAS AF: 0.615

Gnomad4 FIN AF: 0.658

Gnomad4 NFE AF: 0.605

Gnomad4 OTH AF: 0.624

Alfa AF: 0.601 Hom.: 57141

Bravo AF: 0.591

Asia WGS AF: 0.711 AC: 2474 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	2.0
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs754970; hg19: chr11-45051827;