rs1530044

Variant names:

• chr4-165506259-T-A
• rs1530044
• ENST00000747913.1:n.296+126T>A

Variant summary

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

The ENST00000747913.1(ENSG00000297440):​n.296+126T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 152,154 control chromosomes in the GnomAD database, including 13,063 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 0.31 (13063 hom., cov: 33)
• Consequence: ENSG00000297440 ENST00000747913.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.808
• Publications: 9 publications found

Genes affected

ENSG00000297440 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000747913.1. 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
	ENSG00000297440	ENST00000747913.1		n.296+126T>A		intron	N/A
	ENSG00000297440	ENST00000747914.1		n.184+126T>A		intron	N/A
	ENSG00000297440	ENST00000747915.1		n.292+126T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47256 AN: 152036 Hom.: 13016 Cov.: 33

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.311 AC: 47356 AN: 152154 Hom.: 13063 Cov.: 33 AF XY: 0.306 AC XY: 22782 AN XY: 74406

African (AFR) AF: 0.748 AC: 31010 AN: 41468

American (AMR) AF: 0.187 AC: 2860 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 405 AN: 3462

East Asian (EAS) AF: 0.320 AC: 1657 AN: 5180

South Asian (SAS) AF: 0.149 AC: 717 AN: 4820

European-Finnish (FIN) AF: 0.164 AC: 1744 AN: 10604

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8370 AN: 68014

Other (OTH) AF: 0.241 AC: 510 AN: 2112

Alfa AF: 0.235 Hom.: 1027

Bravo AF: 0.332

Asia WGS AF: 0.285 AC: 990 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.9
DANN	Benign	0.47
PhyloP100		0.81

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1530044;

hg19: chr4-166427411;