rs7093778

Variant names:

• chr10-133376816-C-T
• rs7093778
• XR_007062395.1:n.2076G>A

Variant summary

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

The XR_007062395.1(LOC124902563):​n.2076G>A 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 0.746 in 152,184 control chromosomes in the GnomAD database, including 42,924 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 (42924 hom., cov: 34)
• Consequence: LOC124902563 XR_007062395.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.684
• Publications: 2 publications found

Genes affected

LOC124902563 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.911 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902563	XR_007062395.1	n.2076G>A		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000274685	ENST00000621752.2	n.-95G>A		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.746 AC: 113471 AN: 152066 Hom.: 42899 Cov.: 34

Gnomad AFR AF: 0.617

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.801

Gnomad EAS AF: 0.933

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.846

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.792

Gnomad OTH AF: 0.759

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

GnomAD4 genome AF: 0.746 AC: 113527 AN: 152184 Hom.: 42924 Cov.: 34 AF XY: 0.750 AC XY: 55824 AN XY: 74410

African (AFR) AF: 0.617 AC: 25589 AN: 41484

American (AMR) AF: 0.731 AC: 11180 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.801 AC: 2782 AN: 3472

East Asian (EAS) AF: 0.933 AC: 4831 AN: 5176

South Asian (SAS) AF: 0.809 AC: 3904 AN: 4828

European-Finnish (FIN) AF: 0.846 AC: 8969 AN: 10602

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.792 AC: 53891 AN: 68016

Other (OTH) AF: 0.762 AC: 1608 AN: 2110

Alfa AF: 0.764 Hom.: 5560

Bravo AF: 0.731

Asia WGS AF: 0.847 AC: 2946 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.98
DANN	Benign	0.66
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs7093778; hg19: chr10-135190320;