chr11-103527569-C-T

Variant names:

• chr11-103527569-C-T
• rs11826048
• ENST00000827359.1:n.218+2508G>A

Variant summary

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

The ENST00000827359.1(ENSG00000307600):​n.218+2508G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0962 in 152,098 control chromosomes in the GnomAD database, including 722 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 0.096 (722 hom., cov: 32)
• Consequence: ENSG00000307600 ENST00000827359.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.115 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
ENSG00000307600	ENST00000827359.1	n.218+2508G>A		intron_variant	Intron 2 of 2
ENSG00000307600	ENST00000827360.1	n.93-8342G>A		intron_variant	Intron 1 of 1
ENSG00000307600	ENST00000827361.1	n.105+2508G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0961 AC: 14600 AN: 151980 Hom.: 716 Cov.: 32

Gnomad AFR AF: 0.0977

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.0440

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.0787

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0936

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.0962 AC: 14628 AN: 152098 Hom.: 722 Cov.: 32 AF XY: 0.0971 AC XY: 7221 AN XY: 74344

African (AFR) AF: 0.0979 AC: 4062 AN: 41490

American (AMR) AF: 0.109 AC: 1671 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 566 AN: 3470

East Asian (EAS) AF: 0.0437 AC: 226 AN: 5172

South Asian (SAS) AF: 0.123 AC: 594 AN: 4824

European-Finnish (FIN) AF: 0.0787 AC: 832 AN: 10576

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0937 AC: 6368 AN: 67984

Other (OTH) AF: 0.106 AC: 224 AN: 2110

Alfa AF: 0.0922 Hom.: 117

Bravo AF: 0.0965

Asia WGS AF: 0.0920 AC: 321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.56
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs11826048; hg19: chr11-103398297;