ENST00000827359.1:n.218+1113G>T

Variant names:

• chr11-103528964-C-A
• rs10895454
• ENST00000827359.1:n.218+1113G>T

Variant summary

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

The ENST00000827359.1(ENSG00000307600):​n.218+1113G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 152,142 control chromosomes in the GnomAD database, including 13,732 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 0.40 (13732 hom., cov: 33)
• Consequence: ENSG00000307600 ENST00000827359.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.563
• Publications: 4 publications found

Genes affected

ENSG00000307600 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000827359.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307600	ENST00000827359.1		n.218+1113G>T		intron	N/A
	ENSG00000307600	ENST00000827360.1		n.92+7445G>T		intron	N/A
	ENSG00000307600	ENST00000827361.1		n.105+1113G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60589 AN: 152024 Hom.: 13732 Cov.: 33

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.398 AC: 60595 AN: 152142 Hom.: 13732 Cov.: 33 AF XY: 0.393 AC XY: 29228 AN XY: 74364

African (AFR) AF: 0.197 AC: 8191 AN: 41522

American (AMR) AF: 0.366 AC: 5590 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1717 AN: 3468

East Asian (EAS) AF: 0.220 AC: 1142 AN: 5182

South Asian (SAS) AF: 0.353 AC: 1703 AN: 4830

European-Finnish (FIN) AF: 0.481 AC: 5076 AN: 10558

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.526 AC: 35764 AN: 67976

Other (OTH) AF: 0.413 AC: 873 AN: 2116

Alfa AF: 0.337 Hom.: 1454

Bravo AF: 0.382

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.0
DANN	Benign	0.48
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs10895454; hg19: chr11-103399692;