rs1512288

Variant names:

• chr4-144570129-G-A
• rs1512288
• ENST00000649263.1:n.328-154151C>T

Variant summary

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

The ENST00000649263.1(ENSG00000285713):​n.328-154151C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 152,036 control chromosomes in the GnomAD database, including 13,284 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 0.41 (13284 hom., cov: 33)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 15 publications found

Genes affected

ENSG00000285713 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.503 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
ENSG00000285713	ENST00000649263.1	n.328-154151C>T		intron_variant	Intron 4 of 8			ENSP00000497507.1
ENSG00000285783	ENST00000650526.1	n.223-154151C>T		intron_variant	Intron 2 of 14

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62916 AN: 151918 Hom.: 13275 Cov.: 33

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.414 AC: 62963 AN: 152036 Hom.: 13284 Cov.: 33 AF XY: 0.419 AC XY: 31137 AN XY: 74298

African (AFR) AF: 0.407 AC: 16860 AN: 41458

American (AMR) AF: 0.342 AC: 5215 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1259 AN: 3464

East Asian (EAS) AF: 0.301 AC: 1560 AN: 5178

South Asian (SAS) AF: 0.520 AC: 2506 AN: 4822

European-Finnish (FIN) AF: 0.540 AC: 5697 AN: 10558

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.420 AC: 28566 AN: 67982

Other (OTH) AF: 0.378 AC: 797 AN: 2108

Alfa AF: 0.427 Hom.: 8469

Bravo AF: 0.392

Asia WGS AF: 0.385 AC: 1339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.42
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1512288; hg19: chr4-145491281;