ENST00000654627.2:n.291-11261C>T

Variant names:

• chr11-45030276-C-T
• rs754970
• ENST00000654627.2:n.291-11261C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000654627.2(ENSG00000287984):​n.291-11261C>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 ENST00000654627.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.177
• Publications: 3 publications found

Genes affected

ENSG00000287984 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654627.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287984	ENST00000654627.2		n.291-11261C>T		intron	N/A
	ENSG00000294396	ENST00000723346.1		n.121+25659G>A		intron	N/A
	ENSG00000287984	ENST00000723452.1		n.290-11261C>T		intron	N/A

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

African (AFR) AF: 0.555 AC: 23000 AN: 41458

American (AMR) AF: 0.571 AC: 8719 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 2111 AN: 3472

East Asian (EAS) AF: 0.816 AC: 4222 AN: 5174

South Asian (SAS) AF: 0.615 AC: 2969 AN: 4826

European-Finnish (FIN) AF: 0.658 AC: 6960 AN: 10580

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.605 AC: 41117 AN: 67960

Other (OTH) AF: 0.624 AC: 1318 AN: 2112

Alfa AF: 0.600 Hom.: 114157

Bravo AF: 0.591

Asia WGS AF: 0.711 AC: 2474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.0
DANN	Benign	0.66
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs754970; hg19: chr11-45051827;