11-116332072-T-C

Position:

• chr11-116332072-T-C

Variant summary

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

The XR_001748403.2(LOC107987166):​n.350-11633A>G 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 0.0417 in 152,324 control chromosomes in the GnomAD database, including 184 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 0.042 (184 hom., cov: 33)
• Consequence: LOC107987166 XR_001748403.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.527

Genes affected

LOC107987166 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0584 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107987166	XR_001748403.2	n.350-11633A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0418 AC: 6364 AN: 152206 Hom.: 184 Cov.: 33

Gnomad AFR AF: 0.0102

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0570

Gnomad ASJ AF: 0.0271

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0516

Gnomad FIN AF: 0.0461

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0600

Gnomad OTH AF: 0.0458

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

GnomAD4 genome AF: 0.0417 AC: 6359 AN: 152324 Hom.: 184 Cov.: 33 AF XY: 0.0415 AC XY: 3089 AN XY: 74478

Gnomad4 AFR AF: 0.0102

Gnomad4 AMR AF: 0.0566

Gnomad4 ASJ AF: 0.0271

Gnomad4 EAS AF: 0.000965

Gnomad4 SAS AF: 0.0518

Gnomad4 FIN AF: 0.0461

Gnomad4 NFE AF: 0.0600

Gnomad4 OTH AF: 0.0449

Alfa AF: 0.0561 Hom.: 301

Bravo AF: 0.0395

Asia WGS AF: 0.0190 AC: 67 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	13
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12806755; hg19: chr11-116202789;