11-109022119-C-T

Position:

• chr11-109022119-C-T

Variant summary

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

The ENST00000526041.1(ENSG00000255528):​n.225+15624G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,040 control chromosomes in the GnomAD database, including 3,611 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 0.21 (3611 hom., cov: 33)
• Consequence: ENST00000526041.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.796

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000526041.1	n.225+15624G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32005 AN: 151922 Hom.: 3604 Cov.: 33

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.211 AC: 32031 AN: 152040 Hom.: 3611 Cov.: 33 AF XY: 0.211 AC XY: 15688 AN XY: 74288

Gnomad4 AFR AF: 0.265

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.275

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.203

Alfa AF: 0.184 Hom.: 1302

Bravo AF: 0.218

Asia WGS AF: 0.199 AC: 695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	15
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4754373; hg19: chr11-108892846;