rs1554929

chr11-113408042-C-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, non coding transcript 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: ENST00000546284.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000546284.1	n.244+2075C>T		intron_variant, non_coding_transcript_variant		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;