XR_007088699.1:n.197-50296A>G

Variant names:

• chr2-195109799-T-C
• rs1965394
• XR_007088699.1:n.197-50296A>G

Variant summary

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

The XR_007088699.1(LOC105376755):​n.197-50296A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0976 in 151,960 control chromosomes in the GnomAD database, including 1,209 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 0.098 (1209 hom., cov: 32)
• Consequence: LOC105376755 XR_007088699.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 0 publications found

Genes affected

LOC105376755 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.224 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: 0.0976 AC: 14815 AN: 151844 Hom.: 1209 Cov.: 32

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.0604

Gnomad ASJ AF: 0.0505

Gnomad EAS AF: 0.0600

Gnomad SAS AF: 0.0483

Gnomad FIN AF: 0.0402

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0442

Gnomad OTH AF: 0.0841

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

GnomAD4 genome AF: 0.0976 AC: 14828 AN: 151960 Hom.: 1209 Cov.: 32 AF XY: 0.0951 AC XY: 7058 AN XY: 74254

African (AFR) AF: 0.228 AC: 9454 AN: 41428

American (AMR) AF: 0.0603 AC: 919 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.0505 AC: 175 AN: 3464

East Asian (EAS) AF: 0.0595 AC: 306 AN: 5142

South Asian (SAS) AF: 0.0479 AC: 231 AN: 4820

European-Finnish (FIN) AF: 0.0402 AC: 425 AN: 10582

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0442 AC: 3004 AN: 67960

Other (OTH) AF: 0.0837 AC: 177 AN: 2114

Alfa AF: 0.0826 Hom.: 110

Bravo AF: 0.107

Asia WGS AF: 0.0500 AC: 172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.84
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1965394; hg19: chr2-195974523;