rs519982

chr11-118694522-C-T

Variant summary

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

The XR_007062909.1(LOC105369519):n.251+1407C>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 0.318 in 152,020 control chromosomes in the GnomAD database, including 8,108 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 0.32 (8108 hom., cov: 32)
• Consequence: LOC105369519 XR_007062909.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

Genes affected

LOC105369519 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369519	XR_007062909.1	n.251+1407C>T		intron_variant, non_coding_transcript_variant
LOC105369519	XR_007062910.1	n.205+1407C>T		intron_variant, non_coding_transcript_variant
LOC105369519	XR_948068.3	n.342+1407C>T		intron_variant, non_coding_transcript_variant
LOC105369519	XR_948069.3	n.253+1407C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48352 AN: 151902 Hom.: 8094 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.318 AC: 48388 AN: 152020 Hom.: 8108 Cov.: 32 AF XY: 0.318 AC XY: 23662 AN XY: 74300

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.460

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.406

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.327

Gnomad4 OTH AF: 0.335

Alfa AF: 0.319 Hom.: 3652

Bravo AF: 0.334

Asia WGS AF: 0.270 AC: 943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.63
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs519982; hg19: chr11-118565231;