rs11031676

chr11-32264599-C-T

Variant summary

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

The ENST00000525689.2(ENSG00000293378):n.123-34238G>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 0.2 in 152,050 control chromosomes in the GnomAD database, including 3,515 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 0.20 (3515 hom., cov: 32)
• Consequence: ENST00000525689.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0170

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.246 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
	ENST00000525689.2	n.123-34238G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30436 AN: 151932 Hom.: 3514 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.0219

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.200 AC: 30438 AN: 152050 Hom.: 3515 Cov.: 32 AF XY: 0.200 AC XY: 14836 AN XY: 74308

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.0218

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.216

Alfa AF: 0.237 Hom.: 945

Bravo AF: 0.192

Asia WGS AF: 0.0720 AC: 251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	4.6
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11031676; hg19: chr11-32286145;