XR_007066779.1:n.258-2185A>G

Variant names:

• chr1-196925196-T-C
• rs4086175
• XR_007066779.1:n.258-2185A>G

Variant summary

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

The XR_007066779.1(LOC105371675):​n.258-2185A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 150,880 control chromosomes in the GnomAD database, including 4,866 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 0.20 (4866 hom., cov: 32)
• Consequence: LOC105371675 XR_007066779.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.201
• Publications: 11 publications found

Genes affected

LOC105371675 (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 (AFR) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

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: 0.203 AC: 30610 AN: 150770 Hom.: 4857 Cov.: 32

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.0920

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.203 AC: 30633 AN: 150880 Hom.: 4866 Cov.: 32 AF XY: 0.200 AC XY: 14714 AN XY: 73748

African (AFR) AF: 0.413 AC: 16702 AN: 40450

American (AMR) AF: 0.139 AC: 2110 AN: 15172

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 405 AN: 3468

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5178

South Asian (SAS) AF: 0.145 AC: 699 AN: 4824

European-Finnish (FIN) AF: 0.0920 AC: 972 AN: 10564

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9160 AN: 67912

Other (OTH) AF: 0.203 AC: 427 AN: 2106

Alfa AF: 0.162 Hom.: 721

Bravo AF: 0.214

Asia WGS AF: 0.0830 AC: 288 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.2
DANN	Benign	0.47
PhyloP100		0.20
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs4086175; hg19: chr1-196894326;