rs808053

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC105379107 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379107	XR_001742830.2	n.352-4023T>C		intron_variant	Intron 2 of 2
LOC105379107	XR_001742831.2	n.496-4023T>C		intron_variant	Intron 5 of 5
LOC105379107	XR_001742833.2	n.352-4023T>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.272

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.171

Alfa AF: 0.170 Hom.: 256

Bravo AF: 0.186

Asia WGS AF: 0.186 AC: 649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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