rs1554929

Variant names:

• chr11-113408042-C-T
• rs1554929
• ENST00000546284.1:n.244+2075C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000546284.1(ENSG00000256757):​n.244+2075C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 151,960 control chromosomes in the GnomAD database, including 13,283 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 0.37 (13283 hom., cov: 32)
• Consequence: ENSG00000256757 ENST00000546284.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30

Genes affected

ENSG00000256757 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.535 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
ENSG00000256757	ENST00000546284.1	n.244+2075C>T		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55758 AN: 151842 Hom.: 13296 Cov.: 32

Gnomad AFR AF: 0.0979

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.0595

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.367 AC: 55734 AN: 151960 Hom.: 13283 Cov.: 32 AF XY: 0.359 AC XY: 26694 AN XY: 74254

Gnomad4 AFR AF: 0.0976

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.536

Gnomad4 EAS AF: 0.0591

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.446

Gnomad4 NFE AF: 0.539

Gnomad4 OTH AF: 0.421

Alfa AF: 0.509 Hom.: 19683

Bravo AF: 0.347

Asia WGS AF: 0.192 AC: 669 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	0.24
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1554929; hg19: chr11-113278764;