5-75319196-C-T

Variant names:

• chr5-75319196-C-T
• rs17671591
• XR_007058824.1:n.181+1754G>A

Variant summary

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

The XR_007058824.1(LOC124901007):​n.181+1754G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 151,976 control chromosomes in the GnomAD database, including 10,100 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 0.36 (10100 hom., cov: 32)
• Consequence: LOC124901007 XR_007058824.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69
• Publications: 16 publications found

Genes affected

LOC124901007 (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 = 0.537 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: 0.363 AC: 55183 AN: 151858 Hom.: 10087 Cov.: 32

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.363 AC: 55230 AN: 151976 Hom.: 10100 Cov.: 32 AF XY: 0.367 AC XY: 27245 AN XY: 74256

African (AFR) AF: 0.371 AC: 15368 AN: 41414

American (AMR) AF: 0.354 AC: 5409 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.474 AC: 1644 AN: 3470

East Asian (EAS) AF: 0.322 AC: 1664 AN: 5170

South Asian (SAS) AF: 0.555 AC: 2673 AN: 4816

European-Finnish (FIN) AF: 0.356 AC: 3759 AN: 10562

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.346 AC: 23501 AN: 67958

Other (OTH) AF: 0.370 AC: 782 AN: 2112

Alfa AF: 0.354 Hom.: 15824

Bravo AF: 0.356

Asia WGS AF: 0.426 AC: 1481 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	0.86
DANN	Benign	0.71
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs17671591; hg19: chr5-74615021;