11-116826628-C-T

Variant names:

• chr11-116826628-C-T
• rs2071523
• ENST00000814126.1:n.136-1537C>T

Variant summary

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

The ENST00000814126.1(ENSG00000305923):​n.136-1537C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 152,188 control chromosomes in the GnomAD database, including 22,589 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 0.53 (22589 hom., cov: 34)
• Consequence: ENSG00000305923 ENST00000814126.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 11 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000814126.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305923	ENST00000814126.1		n.136-1537C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80362 AN: 152068 Hom.: 22587 Cov.: 34

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.549

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

GnomAD4 genome AF: 0.528 AC: 80386 AN: 152188 Hom.: 22589 Cov.: 34 AF XY: 0.523 AC XY: 38949 AN XY: 74402

African (AFR) AF: 0.321 AC: 13321 AN: 41516

American (AMR) AF: 0.567 AC: 8680 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1911 AN: 3466

East Asian (EAS) AF: 0.615 AC: 3181 AN: 5174

South Asian (SAS) AF: 0.488 AC: 2356 AN: 4826

European-Finnish (FIN) AF: 0.588 AC: 6228 AN: 10592

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.629 AC: 42767 AN: 67996

Other (OTH) AF: 0.549 AC: 1162 AN: 2116

Alfa AF: 0.596 Hom.: 32504

Bravo AF: 0.526

Asia WGS AF: 0.538 AC: 1873 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.096
DANN	Benign	0.70
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs2071523; hg19: chr11-116697344;