rs17315588

Variant names:

• chr11-7892364-C-A
• rs17315588
• ENST00000527847.5:n.354-9431G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000527847.5(ENSG00000254951):​n.354-9431G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0658 in 152,180 control chromosomes in the GnomAD database, including 480 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 0.066 (480 hom., cov: 32)
• Consequence: ENSG00000254951 ENST00000527847.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115
• Publications: 1 publications found

Genes affected

ENSG00000254951 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC283299	NR_036678.1	n.354-9431G>T		intron_variant	Intron 1 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254951	ENST00000527847.5	n.354-9431G>T		intron_variant	Intron 1 of 7	2
ENSG00000254951	ENST00000718815.1	n.374-8272G>T		intron_variant	Intron 2 of 2
ENSG00000254951	ENST00000718816.1	n.45+1708G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0658 AC: 10007 AN: 152062 Hom.: 476 Cov.: 32

Gnomad AFR AF: 0.0194

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.0424

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.0557

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0702

Gnomad OTH AF: 0.0668

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

GnomAD4 genome AF: 0.0658 AC: 10016 AN: 152180 Hom.: 480 Cov.: 32 AF XY: 0.0692 AC XY: 5146 AN XY: 74396

African (AFR) AF: 0.0194 AC: 804 AN: 41532

American (AMR) AF: 0.117 AC: 1786 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0424 AC: 147 AN: 3468

East Asian (EAS) AF: 0.146 AC: 754 AN: 5162

South Asian (SAS) AF: 0.0556 AC: 268 AN: 4822

European-Finnish (FIN) AF: 0.116 AC: 1233 AN: 10590

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0703 AC: 4779 AN: 68006

Other (OTH) AF: 0.0704 AC: 148 AN: 2102

Alfa AF: 0.0682 Hom.: 203

Bravo AF: 0.0666

Asia WGS AF: 0.0970 AC: 338 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	2.4
DANN	Benign	0.60
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs17315588; hg19: chr11-7913911;