rs2434245

Variant names:

• chr5-175780196-C-A
• rs2434245
• XR_007059065.1:n.484+1699G>T

Your query was ambiguous. Multiple possible variants found:

• chr5-175780196-C-A
• chr5-175780196-C-T

Variant summary

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

The XR_007059065.1(LOC124901140):​n.484+1699G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 152,098 control chromosomes in the GnomAD database, including 2,547 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 0.18 (2547 hom., cov: 32)
• Consequence: LOC124901140 XR_007059065.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336
• Publications: 0 publications found

Genes affected

LOC124901140 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27251 AN: 151978 Hom.: 2544 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.0963

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.179 AC: 27260 AN: 152098 Hom.: 2547 Cov.: 32 AF XY: 0.179 AC XY: 13295 AN XY: 74354

African (AFR) AF: 0.146 AC: 6067 AN: 41502

American (AMR) AF: 0.182 AC: 2771 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 559 AN: 3472

East Asian (EAS) AF: 0.0969 AC: 501 AN: 5168

South Asian (SAS) AF: 0.243 AC: 1170 AN: 4812

European-Finnish (FIN) AF: 0.166 AC: 1756 AN: 10568

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.204 AC: 13857 AN: 67988

Other (OTH) AF: 0.181 AC: 384 AN: 2116

Alfa AF: 0.199 Hom.: 1717

Bravo AF: 0.176

Asia WGS AF: 0.178 AC: 618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	11
DANN	Benign	0.64
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs2434245; hg19: chr5-175207199;