chr2-156794268-C-T

Variant names:

• chr2-156794268-C-T
• rs9288624
• ENST00000665531.1:n.45+5493C>T

Variant summary

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

The ENST00000665531.1(ENSG00000287048):​n.45+5493C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 151,948 control chromosomes in the GnomAD database, including 22,496 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 0.52 (22496 hom., cov: 32)
• Consequence: ENSG00000287048 ENST00000665531.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203
• Publications: 6 publications found

Genes affected

ENSG00000287048 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.757 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124907897	XR_007087269.1	n.223+6330C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287048	ENST00000665531.1	n.45+5493C>T		intron_variant	Intron 1 of 1
ENSG00000287048	ENST00000762469.1	n.158+6330C>T		intron_variant	Intron 1 of 4
ENSG00000287048	ENST00000762470.1	n.162+6330C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.521 AC: 79039 AN: 151830 Hom.: 22438 Cov.: 32

Gnomad AFR AF: 0.764

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.521 AC: 79136 AN: 151948 Hom.: 22496 Cov.: 32 AF XY: 0.518 AC XY: 38487 AN XY: 74258

African (AFR) AF: 0.765 AC: 31704 AN: 41468

American (AMR) AF: 0.384 AC: 5853 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1478 AN: 3468

East Asian (EAS) AF: 0.409 AC: 2103 AN: 5146

South Asian (SAS) AF: 0.474 AC: 2286 AN: 4822

European-Finnish (FIN) AF: 0.451 AC: 4760 AN: 10548

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.432 AC: 29317 AN: 67932

Other (OTH) AF: 0.500 AC: 1056 AN: 2112

Alfa AF: 0.458 Hom.: 53435

Bravo AF: 0.523

Asia WGS AF: 0.453 AC: 1579 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.9
DANN	Benign	0.77
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs9288624; hg19: chr2-157650780;