11-61074762-T-C

Variant names:

• chr11-61074762-T-C
• rs757080
• XR_007062690.1:n.1051T>C

Variant summary

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

The XR_007062690.1(LOC124902677):​n.1051T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.708 in 152,064 control chromosomes in the GnomAD database, including 45,091 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 0.71 (45091 hom., cov: 31)
• Consequence: LOC124902677 XR_007062690.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.431
• Publications: 5 publications found

Genes affected

LOC124902677 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.906 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902677	XR_007062690.1	n.1051T>C		non_coding_transcript_exon_variant	Exon 1 of 2
LOC105369325	NR_188502.1	n.62+17535A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303405	ENST00000794255.1	n.135+17535A>G		intron_variant	Intron 1 of 1
ENSG00000303405	ENST00000794256.1	n.136-9806A>G		intron_variant	Intron 1 of 2
ENSG00000303405	ENST00000794257.1	n.132+17535A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107666 AN: 151948 Hom.: 45086 Cov.: 31

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.918

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.896

Gnomad EAS AF: 0.928

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.919

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.901

Gnomad OTH AF: 0.768

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

GnomAD4 genome AF: 0.708 AC: 107683 AN: 152064 Hom.: 45091 Cov.: 31 AF XY: 0.714 AC XY: 53106 AN XY: 74356

African (AFR) AF: 0.224 AC: 9269 AN: 41448

American (AMR) AF: 0.860 AC: 13150 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.896 AC: 3106 AN: 3468

East Asian (EAS) AF: 0.928 AC: 4814 AN: 5186

South Asian (SAS) AF: 0.763 AC: 3680 AN: 4826

European-Finnish (FIN) AF: 0.919 AC: 9692 AN: 10550

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.901 AC: 61264 AN: 67982

Other (OTH) AF: 0.770 AC: 1627 AN: 2114

Alfa AF: 0.747 Hom.: 9455

Bravo AF: 0.689

Asia WGS AF: 0.811 AC: 2809 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.0
DANN	Benign	0.83
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs757080; hg19: chr11-60842234;