2-64268493-G-A

Variant names:

• chr2-64268493-G-A
• rs1529102
• ENST00000717282.1:n.779+8144G>A

Variant summary

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

The ENST00000717282.1(ENSG00000288932):​n.779+8144G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.533 in 152,040 control chromosomes in the GnomAD database, including 21,745 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 0.53 (21745 hom., cov: 32)
• Consequence: ENSG00000288932 ENST00000717282.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126
• Publications: 17 publications found

Genes affected

ENSG00000288932 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.749 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288932	ENST00000717282.1	n.779+8144G>A		intron_variant	Intron 5 of 5
ENSG00000288932	ENST00000717283.1	n.254+38853G>A		intron_variant	Intron 2 of 3
ENSG00000288932	ENST00000717284.1	n.211-22652G>A		intron_variant	Intron 2 of 2
ENSG00000288932	ENST00000717285.1	n.599+5195G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.533 AC: 81016 AN: 151922 Hom.: 21720 Cov.: 32

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.769

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.533 AC: 81106 AN: 152040 Hom.: 21745 Cov.: 32 AF XY: 0.532 AC XY: 39531 AN XY: 74292

African (AFR) AF: 0.554 AC: 22998 AN: 41484

American (AMR) AF: 0.526 AC: 8023 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1758 AN: 3466

East Asian (EAS) AF: 0.769 AC: 3970 AN: 5164

South Asian (SAS) AF: 0.647 AC: 3109 AN: 4802

European-Finnish (FIN) AF: 0.498 AC: 5256 AN: 10560

Middle Eastern (MID) AF: 0.411 AC: 120 AN: 292

European-Non Finnish (NFE) AF: 0.505 AC: 34358 AN: 67990

Other (OTH) AF: 0.509 AC: 1078 AN: 2116

Alfa AF: 0.518 Hom.: 86267

Bravo AF: 0.539

Asia WGS AF: 0.717 AC: 2485 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	8.7
DANN	Benign	0.74
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs1529102; hg19: chr2-64495627;