rs17309979

chr11-27831302-G-A

Variant summary

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

The ENST00000530663.1(ENSG00000255496):n.147+46200C>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 0.11 in 152,178 control chromosomes in the GnomAD database, including 1,264 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 0.11 (1264 hom., cov: 32)
• Consequence: ENST00000530663.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.163 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
	ENST00000530663.1	n.147+46200C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16766 AN: 152060 Hom.: 1265 Cov.: 32

Gnomad AFR AF: 0.0282

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0203

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.110 AC: 16750 AN: 152178 Hom.: 1264 Cov.: 32 AF XY: 0.109 AC XY: 8076 AN XY: 74414

Gnomad4 AFR AF: 0.0281

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.0202

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.115

Alfa AF: 0.129 Hom.: 293

Bravo AF: 0.103

Asia WGS AF: 0.0180 AC: 66 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.4
Dann	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17309979; hg19: chr11-27852849;