rs1552104

Variant names:

• chr5-126124880-A-G
• rs1552104
• ENST00000450613.2:n.72-26719T>C

Variant summary

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

The ENST00000450613.2(ENSG00000248752):​n.72-26719T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 151,932 control chromosomes in the GnomAD database, including 19,561 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 0.50 (19561 hom., cov: 31)
• Consequence: ENSG00000248752 ENST00000450613.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 2 publications found

Genes affected

ENSG00000248752 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901056	XR_007058919.1	n.1620-26719T>C		intron_variant	Intron 1 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248752	ENST00000450613.2	n.72-26719T>C		intron_variant	Intron 1 of 2	3
ENSG00000248752	ENST00000651847.1	n.153-26719T>C		intron_variant	Intron 2 of 15
ENSG00000248752	ENST00000781629.1	n.251-26719T>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76170 AN: 151814 Hom.: 19557 Cov.: 31

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.634

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.501 AC: 76191 AN: 151932 Hom.: 19561 Cov.: 31 AF XY: 0.503 AC XY: 37357 AN XY: 74270

African (AFR) AF: 0.415 AC: 17175 AN: 41428

American (AMR) AF: 0.475 AC: 7260 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.589 AC: 2043 AN: 3470

East Asian (EAS) AF: 0.311 AC: 1609 AN: 5174

South Asian (SAS) AF: 0.466 AC: 2241 AN: 4812

European-Finnish (FIN) AF: 0.634 AC: 6688 AN: 10542

Middle Eastern (MID) AF: 0.545 AC: 159 AN: 292

European-Non Finnish (NFE) AF: 0.551 AC: 37418 AN: 67918

Other (OTH) AF: 0.510 AC: 1078 AN: 2114

Alfa AF: 0.536 Hom.: 11271

Bravo AF: 0.485

Asia WGS AF: 0.373 AC: 1297 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.3
DANN	Benign	0.69
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs1552104; hg19: chr5-125460573;