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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377520	XR_939419.2	n.233+126T>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297440	ENST00000747913.1	n.296+126T>A		intron_variant	Intron 3 of 3
ENSG00000297440	ENST00000747914.1	n.184+126T>A		intron_variant	Intron 2 of 2
ENSG00000297440	ENST00000747915.1	n.292+126T>A		intron_variant	Intron 3 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs1530044; hg19: chr4-166427411;