rs1549681

Variant names:

• chr5-36537972-A-G
• rs1549681
• ENST00000751409.1:n.110+15185T>C

Variant summary

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

The ENST00000751409.1(ENSG00000297854):​n.110+15185T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 152,124 control chromosomes in the GnomAD database, including 16,688 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 (16688 hom., cov: 33)
• Consequence: ENSG00000297854 ENST00000751409.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.54
• Publications: 1 publications found

Genes affected

ENSG00000297854 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.71 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
ENSG00000297854	ENST00000751409.1	n.110+15185T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65462 AN: 152006 Hom.: 16641 Cov.: 33

Gnomad AFR AF: 0.717

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.431 AC: 65568 AN: 152124 Hom.: 16688 Cov.: 33 AF XY: 0.425 AC XY: 31632 AN XY: 74370

African (AFR) AF: 0.717 AC: 29759 AN: 41492

American (AMR) AF: 0.306 AC: 4672 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1119 AN: 3470

East Asian (EAS) AF: 0.119 AC: 617 AN: 5178

South Asian (SAS) AF: 0.282 AC: 1362 AN: 4826

European-Finnish (FIN) AF: 0.360 AC: 3809 AN: 10576

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.338 AC: 22967 AN: 67988

Other (OTH) AF: 0.403 AC: 851 AN: 2114

Alfa AF: 0.354 Hom.: 16187

Bravo AF: 0.435

Asia WGS AF: 0.259 AC: 901 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.52
DANN	Benign	0.57
PhyloP100		-4.5

Splicing

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

Other links and lift over

dbSNP: rs1549681; hg19: chr5-36538074;