rs1489759

Variant names:

• chr4-144553321-A-G
• rs1489759
• ENST00000649263.1:n.328-137343T>C

Variant summary

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

The ENST00000649263.1(ENSG00000285713):​n.328-137343T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 152,090 control chromosomes in the GnomAD database, including 14,376 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 0.43 (14376 hom., cov: 32)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.513
• Publications: 24 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649263.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285713	ENST00000649263.1		n.328-137343T>C		intron	N/A	ENSP00000497507.1	A0A3B3ISY7
	ENSG00000285783	ENST00000650526.1		n.223-137343T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65328 AN: 151972 Hom.: 14361 Cov.: 32

Gnomad AFR AF: 0.479

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.430 AC: 65377 AN: 152090 Hom.: 14376 Cov.: 32 AF XY: 0.434 AC XY: 32251 AN XY: 74322

African (AFR) AF: 0.479 AC: 19878 AN: 41492

American (AMR) AF: 0.342 AC: 5223 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1263 AN: 3472

East Asian (EAS) AF: 0.299 AC: 1550 AN: 5176

South Asian (SAS) AF: 0.493 AC: 2378 AN: 4824

European-Finnish (FIN) AF: 0.536 AC: 5659 AN: 10566

Middle Eastern (MID) AF: 0.397 AC: 116 AN: 292

European-Non Finnish (NFE) AF: 0.414 AC: 28144 AN: 67978

Other (OTH) AF: 0.382 AC: 807 AN: 2110

Alfa AF: 0.418 Hom.: 33208

Bravo AF: 0.410

Asia WGS AF: 0.384 AC: 1337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.3
DANN	Benign	0.64
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs1489759; hg19: chr4-145474473;