rs11621263

chr14-24625944-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+2818C>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 0.146 in 152,122 control chromosomes in the GnomAD database, including 1,709 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 0.15 (1709 hom., cov: 32)
• Consequence: ENST00000555300.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.218 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+2818C>T		intron_variant, non_coding_transcript_variant		5
	ENST00000557736.5	n.439+2818C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22151 AN: 152004 Hom.: 1701 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.146 AC: 22185 AN: 152122 Hom.: 1709 Cov.: 32 AF XY: 0.146 AC XY: 10820 AN XY: 74356

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.143

Gnomad4 OTH AF: 0.154

Alfa AF: 0.148 Hom.: 303

Bravo AF: 0.144

Asia WGS AF: 0.190 AC: 659 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	5.7
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11621263; hg19: chr14-25095150;