rs17101477

chr11-103736010-G-A

Variant summary

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

The ENST00000533459.1(ENSG00000254987):n.128-31112C>T 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 0.0523 in 152,260 control chromosomes in the GnomAD database, including 423 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 0.052 (423 hom., cov: 32)
• Consequence: ENST00000533459.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.301

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 (EAS) allele frequency at 95% confidence interval = 0.16 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
	ENST00000533459.1	n.128-31112C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0523 AC: 7956 AN: 152144 Hom.: 419 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0315

Gnomad ASJ AF: 0.0130

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.0515

Gnomad FIN AF: 0.00998

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0149

Gnomad OTH AF: 0.0435

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

GnomAD4 genome AF: 0.0523 AC: 7970 AN: 152260 Hom.: 423 Cov.: 32 AF XY: 0.0521 AC XY: 3881 AN XY: 74438

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.0314

Gnomad4 ASJ AF: 0.0130

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.0518

Gnomad4 FIN AF: 0.00998

Gnomad4 NFE AF: 0.0149

Gnomad4 OTH AF: 0.0425

Alfa AF: 0.0235 Hom.: 139

Bravo AF: 0.0576

Asia WGS AF: 0.101 AC: 349 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	0.97
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17101477; hg19: chr11-103606738;