11-33903240-A-G

Position:

• chr11-33903240-A-G

Variant summary

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

The XR_931176.3(LOC105376621):​n.91-3369A>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 0.637 in 151,938 control chromosomes in the GnomAD database, including 31,019 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 0.64 (31019 hom., cov: 30)
• Consequence: LOC105376621 XR_931176.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.227

Genes affected

LOC105376621 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376621	XR_931176.3	n.91-3369A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96778 AN: 151820 Hom.: 30999 Cov.: 30

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.632

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

GnomAD4 genome AF: 0.637 AC: 96832 AN: 151938 Hom.: 31019 Cov.: 30 AF XY: 0.633 AC XY: 47039 AN XY: 74260

Gnomad4 AFR AF: 0.678

Gnomad4 AMR AF: 0.548

Gnomad4 ASJ AF: 0.584

Gnomad4 EAS AF: 0.592

Gnomad4 SAS AF: 0.556

Gnomad4 FIN AF: 0.668

Gnomad4 NFE AF: 0.640

Gnomad4 OTH AF: 0.625

Alfa AF: 0.634 Hom.: 30272

Bravo AF: 0.632

Asia WGS AF: 0.520 AC: 1809 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.0
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs941940; hg19: chr11-33924787;