11-61074762-T-C

Position:

• chr11-61074762-T-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC124902677 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC124902677	XR_007062690.1	n.1051T>C		non_coding_transcript_exon_variant	1/2
		n.61074762T>C		intergenic_region
LOC105369325	NR_188502.1	n.62+17535A>G		intron_variant

Ensembl

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

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

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.860

Gnomad4 ASJ AF: 0.896

Gnomad4 EAS AF: 0.928

Gnomad4 SAS AF: 0.763

Gnomad4 FIN AF: 0.919

Gnomad4 NFE AF: 0.901

Gnomad4 OTH AF: 0.770

Alfa AF: 0.761 Hom.: 9432

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs757080; hg19: chr11-60842234;