chr10-133376854-C-G

Variant names:

• chr10-133376854-C-G
• rs11101721
• XR_007062395.1:n.2038G>C

Variant summary

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

The XR_007062395.1(LOC124902563):​n.2038G>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 0.0937 in 152,252 control chromosomes in the GnomAD database, including 1,055 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 0.094 (1055 hom., cov: 34)
• Consequence: LOC124902563 XR_007062395.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.724
• Publications: 6 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000621752.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000274685	ENST00000621752.2	TSL:6	n.-133G>C		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.0936 AC: 14242 AN: 152134 Hom.: 1050 Cov.: 34

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.0616

Gnomad ASJ AF: 0.0890

Gnomad EAS AF: 0.0233

Gnomad SAS AF: 0.0561

Gnomad FIN AF: 0.0250

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0498

Gnomad OTH AF: 0.0791

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

GnomAD4 genome AF: 0.0937 AC: 14269 AN: 152252 Hom.: 1055 Cov.: 34 AF XY: 0.0914 AC XY: 6803 AN XY: 74442

African (AFR) AF: 0.209 AC: 8686 AN: 41522

American (AMR) AF: 0.0616 AC: 942 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0890 AC: 309 AN: 3472

East Asian (EAS) AF: 0.0233 AC: 121 AN: 5184

South Asian (SAS) AF: 0.0555 AC: 268 AN: 4828

European-Finnish (FIN) AF: 0.0250 AC: 266 AN: 10620

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0498 AC: 3390 AN: 68018

Other (OTH) AF: 0.0783 AC: 165 AN: 2108

Alfa AF: 0.0172 Hom.: 7

Bravo AF: 0.103

Asia WGS AF: 0.0480 AC: 169 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	0.47
DANN	Benign	0.41
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs11101721; hg19: chr10-135190358;