5-131407848-C-T

Variant names:

• chr5-131407848-C-T
• rs27708
• XR_007058929.1:n.3160G>A

Variant summary

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

The XR_007058929.1(LOC105379173):​n.3160G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 152,118 control chromosomes in the GnomAD database, including 4,244 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 0.23 (4244 hom., cov: 32)
• Consequence: LOC105379173 XR_007058929.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.630
• Publications: 0 publications found

Genes affected

LOC105379173 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.471 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: 0.228 AC: 34712 AN: 152000 Hom.: 4235 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.191

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.229 AC: 34767 AN: 152118 Hom.: 4244 Cov.: 32 AF XY: 0.238 AC XY: 17669 AN XY: 74348

African (AFR) AF: 0.198 AC: 8236 AN: 41530

American (AMR) AF: 0.250 AC: 3830 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 986 AN: 3468

East Asian (EAS) AF: 0.486 AC: 2512 AN: 5164

South Asian (SAS) AF: 0.254 AC: 1227 AN: 4822

European-Finnish (FIN) AF: 0.362 AC: 3816 AN: 10552

Middle Eastern (MID) AF: 0.192 AC: 56 AN: 292

European-Non Finnish (NFE) AF: 0.197 AC: 13410 AN: 67978

Other (OTH) AF: 0.213 AC: 449 AN: 2110

Alfa AF: 0.211 Hom.: 695

Bravo AF: 0.221

Asia WGS AF: 0.371 AC: 1292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.60
DANN	Benign	0.66
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs27708; hg19: chr5-130743541;