XR_935106.3:n.181-2680T>C

Variant names:

• chr18-3465134-A-G
• rs58882377
• XR_935106.3:n.181-2680T>C

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The XR_935106.3(LOC105371965):​n.181-2680T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 140,404 control chromosomes in the GnomAD database, including 3,720 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 0.21 (3720 hom., cov: 28)
• Consequence: LOC105371965 XR_935106.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.21
• Publications: 3 publications found

Genes affected

LOC105371965 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BS2: High Homozygotes in GnomAd4 at 3720 gene

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.207 AC: 29002 AN: 140280 Hom.: 3709 Cov.: 28

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.0690

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.141

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.207 AC: 29039 AN: 140404 Hom.: 3720 Cov.: 28 AF XY: 0.204 AC XY: 13907 AN XY: 68220

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.333 AC: 12804 AN: 38466

American (AMR) AF: 0.120 AC: 1722 AN: 14380

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 682 AN: 3270

East Asian (EAS) AF: 0.136 AC: 679 AN: 4980

South Asian (SAS) AF: 0.145 AC: 633 AN: 4364

European-Finnish (FIN) AF: 0.201 AC: 1799 AN: 8934

Middle Eastern (MID) AF: 0.144 AC: 39 AN: 270

European-Non Finnish (NFE) AF: 0.164 AC: 10300 AN: 62904

Other (OTH) AF: 0.163 AC: 321 AN: 1966

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.196 Hom.: 360

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.62
DANN	Benign	0.030
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs58882377; hg19: chr18-3465132;