rs11621263

Variant names:

• chr14-24625944-C-T
• rs11621263
• ENST00000555300.1:n.177+2818C>T

Variant summary

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

The ENST00000557736.5(ENSG00000258657):​n.439+2818C>T variant causes a intron 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: ENSG00000258657 ENST00000557736.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116

Genes affected

ENSG00000258657 (HGNC:58166):

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000258657	ENST00000555300.1	n.177+2818C>T		intron_variant	Intron 2 of 3	5
ENSG00000258657	ENST00000557736.5	n.439+2818C>T		intron_variant	Intron 2 of 2	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;