rs11034653

chr11-38267043-C-T

Variant summary

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

The XR_931202.2(LOC105376634):n.554+58132G>A 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 0.0865 in 152,042 control chromosomes in the GnomAD database, including 1,832 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 0.086 (1832 hom., cov: 32)
• Consequence: LOC105376634 XR_931202.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.272

Genes affected

LOC105376634 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376634	XR_931202.2	n.554+58132G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0862 AC: 13100 AN: 151924 Hom.: 1823 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0319

Gnomad ASJ AF: 0.00894

Gnomad EAS AF: 0.0235

Gnomad SAS AF: 0.00788

Gnomad FIN AF: 0.00472

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00572

Gnomad OTH AF: 0.0653

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

GnomAD4 genome AF: 0.0865 AC: 13145 AN: 152042 Hom.: 1832 Cov.: 32 AF XY: 0.0833 AC XY: 6190 AN XY: 74324

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.0318

Gnomad4 ASJ AF: 0.00894

Gnomad4 EAS AF: 0.0234

Gnomad4 SAS AF: 0.00830

Gnomad4 FIN AF: 0.00472

Gnomad4 NFE AF: 0.00572

Gnomad4 OTH AF: 0.0651

Alfa AF: 0.0198 Hom.: 254

Bravo AF: 0.0973

Asia WGS AF: 0.0340 AC: 120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	4.5
Dann	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11034653; hg19: chr11-38288593;