rs17315588

Positions:

• chr11-7892364-C-A

Variant summary

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

The NR_036678.1(LOC283299):​n.354-9431G>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 0.0658 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: LOC283299 NR_036678.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115

Genes affected

LOC283299 (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 (EAS) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC283299	NR_036678.1	n.354-9431G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000527847.5	n.354-9431G>T		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.0194

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.0424

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.0556

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.0703

Gnomad4 OTH AF: 0.0704

Alfa AF: 0.0683 Hom.: 185

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17315588; hg19: chr11-7913911;