rs1263177

Variant names:

• chr11-116819996-C-T
• rs1263177
• ENST00000814126.1:n.135+5656C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000814126.1(ENSG00000305923):​n.135+5656C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 151,856 control chromosomes in the GnomAD database, including 28,721 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 0.61 (28721 hom., cov: 31)
• Consequence: ENSG00000305923 ENST00000814126.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 7 publications found

Genes affected

ENSG00000305923 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.625 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
ENSG00000305923	ENST00000814126.1	n.135+5656C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93297 AN: 151738 Hom.: 28722 Cov.: 31

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.615 AC: 93326 AN: 151856 Hom.: 28721 Cov.: 31 AF XY: 0.607 AC XY: 45068 AN XY: 74246

African (AFR) AF: 0.619 AC: 25613 AN: 41386

American (AMR) AF: 0.602 AC: 9194 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.559 AC: 1938 AN: 3464

East Asian (EAS) AF: 0.614 AC: 3154 AN: 5140

South Asian (SAS) AF: 0.495 AC: 2384 AN: 4812

European-Finnish (FIN) AF: 0.586 AC: 6190 AN: 10558

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.630 AC: 42771 AN: 67918

Other (OTH) AF: 0.615 AC: 1296 AN: 2106

Alfa AF: 0.631 Hom.: 41181

Bravo AF: 0.626

Asia WGS AF: 0.552 AC: 1924 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.26
DANN	Benign	0.67
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1263177; hg19: chr11-116690712;