11-61046160-C-G

Variant names:

• chr11-61046160-C-G
• rs4938993
• ENST00000794255.1:n.136-32620G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_188502.1(LOC105369325):​n.63-15765G>C variant causes a intron 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 NR_188502.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 2 publications found

Genes affected

ENSG00000303405 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_188502.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105369325	NR_188502.1		n.63-15765G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303405	ENST00000794255.1		n.136-32620G>C		intron	N/A
	ENSG00000303405	ENST00000794256.1		n.228+18704G>C		intron	N/A
	ENSG00000303405	ENST00000794257.1		n.133-2878G>C		intron	N/A

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

African (AFR) AF: 0.637 AC: 26306 AN: 41328

American (AMR) AF: 0.785 AC: 11986 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.770 AC: 2674 AN: 3472

East Asian (EAS) AF: 0.889 AC: 4579 AN: 5150

South Asian (SAS) AF: 0.917 AC: 4414 AN: 4816

European-Finnish (FIN) AF: 0.824 AC: 8695 AN: 10548

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.782 AC: 53135 AN: 67938

Other (OTH) AF: 0.747 AC: 1572 AN: 2104

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.40
DANN	Benign	0.40
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4938993; hg19: chr11-60813632;