rs1363258

chr5-103933993-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001742831.2(LOC105379107):n.924A>C 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 0.336 in 151,982 control chromosomes in the GnomAD database, including 9,425 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 0.34 (9425 hom., cov: 32)
• Consequence: LOC105379107 XR_001742831.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.556

Genes affected

LOC105379107 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379107	XR_001742831.2	n.924A>C		non_coding_transcript_exon_variant	6/6
LOC105379107	XR_001742830.2	n.780A>C		non_coding_transcript_exon_variant	3/3
LOC105379107	XR_001742832.1	n.619A>C		non_coding_transcript_exon_variant	3/3
LOC105379107	XR_001742833.2	n.759+21A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51093 AN: 151864 Hom.: 9423 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.336 AC: 51104 AN: 151982 Hom.: 9425 Cov.: 32 AF XY: 0.332 AC XY: 24633 AN XY: 74266

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.282

Gnomad4 ASJ AF: 0.350

Gnomad4 EAS AF: 0.159

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.421

Gnomad4 NFE AF: 0.424

Gnomad4 OTH AF: 0.349

Alfa AF: 0.400 Hom.: 26791

Bravo AF: 0.317

Asia WGS AF: 0.223 AC: 777 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.2
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1363258; hg19: chr5-103269694;