rs494459

chr11-118703966-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.252-642C>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 0.399 in 151,702 control chromosomes in the GnomAD database, including 12,430 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 0.40 (12430 hom., cov: 30)
• Consequence: LOC105369519 XR_007062909.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.109

Genes affected

LOC105369519 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369519	XR_007062909.1	n.252-642C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000646572.2	n.230-642C>T		intron_variant, non_coding_transcript_variant
	ENST00000702882.1	n.230-713C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60464 AN: 151582 Hom.: 12414 Cov.: 30

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.399 AC: 60525 AN: 151702 Hom.: 12430 Cov.: 30 AF XY: 0.396 AC XY: 29386 AN XY: 74114

Gnomad4 AFR AF: 0.367

Gnomad4 AMR AF: 0.519

Gnomad4 ASJ AF: 0.396

Gnomad4 EAS AF: 0.377

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.411

Alfa AF: 0.403 Hom.: 25791

Bravo AF: 0.414

Asia WGS AF: 0.292 AC: 1017 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	5.0
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs494459; hg19: chr11-118574675;