rs11629129

chr14-24625650-C-T

Variant summary

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

The ENST00000555300.1(ENSG00000258657):n.177+2524C>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 0.0836 in 152,300 control chromosomes in the GnomAD database, including 555 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 0.084 (555 hom., cov: 33)
• Consequence: ENST00000555300.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.292

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 (SAS) allele frequency at 95% confidence interval = 0.123 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
	ENST00000555300.1	n.177+2524C>T		intron_variant, non_coding_transcript_variant		5
	ENST00000557736.5	n.439+2524C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0836 AC: 12725 AN: 152182 Hom.: 550 Cov.: 33

Gnomad AFR AF: 0.0672

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.0671

Gnomad ASJ AF: 0.0760

Gnomad EAS AF: 0.0607

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.0741

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0970

Gnomad OTH AF: 0.0951

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

GnomAD4 genome AF: 0.0836 AC: 12737 AN: 152300 Hom.: 555 Cov.: 33 AF XY: 0.0825 AC XY: 6143 AN XY: 74468

Gnomad4 AFR AF: 0.0673

Gnomad4 AMR AF: 0.0669

Gnomad4 ASJ AF: 0.0760

Gnomad4 EAS AF: 0.0611

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.0741

Gnomad4 NFE AF: 0.0970

Gnomad4 OTH AF: 0.0937

Alfa AF: 0.0972 Hom.: 1029

Bravo AF: 0.0816

Asia WGS AF: 0.0750 AC: 261 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	1.2
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11629129; hg19: chr14-25094856;