ENST00000654627.2:n.501-281G>A

Variant names:

• chr11-45043414-G-A
• rs7121790
• ENST00000654627.2:n.501-281G>A

Variant summary

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

The ENST00000654627.2(ENSG00000287984):​n.501-281G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,238 control chromosomes in the GnomAD database, including 2,370 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 0.15 (2370 hom., cov: 33)
• Consequence: ENSG00000287984 ENST00000654627.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.839
• Publications: 0 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376650	XR_931237.3	n.691-281G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287984	ENST00000654627.2	n.501-281G>A		intron_variant	Intron 2 of 2
ENSG00000294396	ENST00000723346.1	n.121+12521C>T		intron_variant	Intron 1 of 1
ENSG00000287984	ENST00000723452.1	n.500-274G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23287 AN: 152120 Hom.: 2372 Cov.: 33

Gnomad AFR AF: 0.0438

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0841

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.153 AC: 23274 AN: 152238 Hom.: 2370 Cov.: 33 AF XY: 0.149 AC XY: 11114 AN XY: 74432

African (AFR) AF: 0.0437 AC: 1816 AN: 41584

American (AMR) AF: 0.142 AC: 2166 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 622 AN: 3472

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5190

South Asian (SAS) AF: 0.0838 AC: 404 AN: 4822

European-Finnish (FIN) AF: 0.225 AC: 2382 AN: 10584

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15264 AN: 67976

Other (OTH) AF: 0.161 AC: 340 AN: 2110

Alfa AF: 0.197 Hom.: 10451

Bravo AF: 0.144

Asia WGS AF: 0.0490 AC: 171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.3
DANN	Benign	0.44
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs7121790; hg19: chr11-45064965;