rs11108526

Variant names:

• chr12-96461992-C-T
• rs11108526
• ENST00000548740.1:n.226+21458G>A

Variant summary

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

The ENST00000548740.1(ENSG00000258272):​n.226+21458G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,116 control chromosomes in the GnomAD database, including 1,369 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 0.10 (1369 hom., cov: 32)
• Consequence: ENSG00000258272 ENST00000548740.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74

Genes affected

ENSG00000258272 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.403 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
ENSG00000258272	ENST00000548740.1	n.226+21458G>A		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15599 AN: 151998 Hom.: 1365 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.0736

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.0363

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.0544

Gnomad FIN AF: 0.0862

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0451

Gnomad OTH AF: 0.0915

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

GnomAD4 genome AF: 0.103 AC: 15629 AN: 152116 Hom.: 1369 Cov.: 32 AF XY: 0.107 AC XY: 7961 AN XY: 74358

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.0363

Gnomad4 EAS AF: 0.418

Gnomad4 SAS AF: 0.0546

Gnomad4 FIN AF: 0.0862

Gnomad4 NFE AF: 0.0450

Gnomad4 OTH AF: 0.0929

Alfa AF: 0.0879 Hom.: 161

Bravo AF: 0.113

Asia WGS AF: 0.230 AC: 802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.32
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11108526; hg19: chr12-96855770;