chr18-3465134-A-G

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371965	XR_935106.3	n.181-2680T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 = 0.000000), 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 v4.3

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;