rs11079110

Positions:

• chr17-54186380-G-A
• chr17-54186380-G-C
• chr17-54186380-G-T

Variant summary

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

The ENST00000652614.1(ENSG00000285939):​n.294+31541C>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 0.473 in 152,010 control chromosomes in the GnomAD database, including 19,832 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 0.47 (19832 hom., cov: 32)
• Consequence: ENST00000652614.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360

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 = 0.6 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000652614.1	n.294+31541C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.474 AC: 71937 AN: 151892 Hom.: 19831 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.473 AC: 71950 AN: 152010 Hom.: 19832 Cov.: 32 AF XY: 0.477 AC XY: 35441 AN XY: 74266

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.465

Gnomad4 ASJ AF: 0.568

Gnomad4 EAS AF: 0.543

Gnomad4 SAS AF: 0.530

Gnomad4 FIN AF: 0.683

Gnomad4 NFE AF: 0.605

Gnomad4 OTH AF: 0.521

Alfa AF: 0.575 Hom.: 16084

Bravo AF: 0.447

Asia WGS AF: 0.496 AC: 1721 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	0.77
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11079110; hg19: chr17-52263741;