rs11605096

chr11-113671388-C-A

Variant summary

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

The XR_001748391.2(LOC107984390):n.5178+9945G>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 0.0807 in 152,148 control chromosomes in the GnomAD database, including 645 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 0.081 (645 hom., cov: 32)
• Consequence: LOC107984390 XR_001748391.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

Genes affected

LOC107984390 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984390	XR_001748391.2	n.5178+9945G>T		intron_variant, non_coding_transcript_variant
LOC107984390	XR_001748390.2	n.5178+9945G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0808 AC: 12278 AN: 152030 Hom.: 644 Cov.: 32

Gnomad AFR AF: 0.0229

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.0433

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0673

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.0726

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

GnomAD4 genome AF: 0.0807 AC: 12277 AN: 152148 Hom.: 645 Cov.: 32 AF XY: 0.0791 AC XY: 5882 AN XY: 74378

Gnomad4 AFR AF: 0.0228

Gnomad4 AMR AF: 0.0998

Gnomad4 ASJ AF: 0.0433

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0676

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.0714

Alfa AF: 0.0926 Hom.: 102

Bravo AF: 0.0753

Asia WGS AF: 0.0360 AC: 126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.18
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11605096; hg19: chr11-113542110;