chr11-61046160-C-G

Position:

• chr11-61046160-C-G

Variant summary

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

The XR_950154.3(LOC105369325):​n.63-15765G>C 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 0.752 in 151,832 control chromosomes in the GnomAD database, including 43,343 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 0.75 (43343 hom., cov: 29)
• Consequence: LOC105369325 XR_950154.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

Genes affected

LOC105369325 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.894 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369325	XR_950154.3	n.63-15765G>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.752 AC: 114026 AN: 151714 Hom.: 43296 Cov.: 29

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.917

Gnomad FIN AF: 0.824

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.782

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.752 AC: 114129 AN: 151832 Hom.: 43343 Cov.: 29 AF XY: 0.758 AC XY: 56274 AN XY: 74220

Gnomad4 AFR AF: 0.637

Gnomad4 AMR AF: 0.785

Gnomad4 ASJ AF: 0.770

Gnomad4 EAS AF: 0.889

Gnomad4 SAS AF: 0.917

Gnomad4 FIN AF: 0.824

Gnomad4 NFE AF: 0.782

Gnomad4 OTH AF: 0.747

Alfa AF: 0.763 Hom.: 5516

Bravo AF: 0.741

Asia WGS AF: 0.876 AC: 3047 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.40
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4938993; hg19: chr11-60813632;