rs808053

Variant names:

• chr5-103929542-T-C
• rs808053
• XR_001742830.2:n.352-4023T>C

Variant summary

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

The XR_001742830.2(LOC105379107):​n.352-4023T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,058 control chromosomes in the GnomAD database, including 2,526 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 (2526 hom., cov: 31)
• Consequence: LOC105379107 XR_001742830.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700
• Publications: 0 publications found

Genes affected

LOC105379107 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.26 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: 0.180 AC: 27332 AN: 151940 Hom.: 2523 Cov.: 31

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.180 AC: 27345 AN: 152058 Hom.: 2526 Cov.: 31 AF XY: 0.179 AC XY: 13274 AN XY: 74326

African (AFR) AF: 0.225 AC: 9334 AN: 41456

American (AMR) AF: 0.195 AC: 2975 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 588 AN: 3470

East Asian (EAS) AF: 0.272 AC: 1402 AN: 5154

South Asian (SAS) AF: 0.140 AC: 672 AN: 4808

European-Finnish (FIN) AF: 0.128 AC: 1351 AN: 10580

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10522 AN: 67986

Other (OTH) AF: 0.171 AC: 360 AN: 2110

Alfa AF: 0.172 Hom.: 270

Bravo AF: 0.186

Asia WGS AF: 0.186 AC: 649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.7
DANN	Benign	0.55
PhyloP100		0.070

Splicing

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

Other links and lift over

dbSNP: rs808053; hg19: chr5-103265243; COSMIC: COSV60175811;