rs17309979

Variant names:

• chr11-27831302-G-A
• rs17309979
• ENST00000530663.1:n.147+46200C>T

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 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: ENSG00000255496 ENST00000530663.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460

Genes affected

ENSG00000255496 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000255496	ENST00000530663.1	n.147+46200C>T		intron_variant	Intron 1 of 1	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;