rs2959025

Variant names:

• chr8-104467952-A-G
• rs2959025
• XR_928507.3:n.219-1775A>G

Your query was ambiguous. Multiple possible variants found:

• chr8-104467952-A-G
• chr8-104467952-A-T

Variant summary

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

The XR_928507.3(LOC105375691):​n.219-1775A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 152,192 control chromosomes in the GnomAD database, including 6,685 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 0.28 (6685 hom., cov: 32)
• Consequence: LOC105375691 XR_928507.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.261
• Publications: 7 publications found

Genes affected

LOC105375691 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.393 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: 0.277 AC: 42191 AN: 152076 Hom.: 6689 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.277 AC: 42209 AN: 152192 Hom.: 6685 Cov.: 32 AF XY: 0.279 AC XY: 20758 AN XY: 74400

African (AFR) AF: 0.119 AC: 4956 AN: 41544

American (AMR) AF: 0.263 AC: 4018 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1322 AN: 3468

East Asian (EAS) AF: 0.407 AC: 2102 AN: 5164

South Asian (SAS) AF: 0.363 AC: 1749 AN: 4816

European-Finnish (FIN) AF: 0.308 AC: 3264 AN: 10588

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.350 AC: 23819 AN: 67996

Other (OTH) AF: 0.293 AC: 620 AN: 2116

Alfa AF: 0.336 Hom.: 17711

Bravo AF: 0.265

Asia WGS AF: 0.347 AC: 1209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.3
DANN	Benign	0.74
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs2959025; hg19: chr8-105480180; COSMIC: COSV107415461;