rs1363258

Variant names:

• chr5-103933993-A-C
• rs1363258
• XR_001742830.2:n.780A>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.780A>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_001742830.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.556
• Publications: 6 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=-0.95).
• 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 rank	MANE	Protein	UniProt
LOC105379107	XR_001742830.2	n.780A>C		non_coding_transcript_exon_variant	Exon 3 of 3
LOC105379107	XR_001742831.2	n.924A>C		non_coding_transcript_exon_variant	Exon 6 of 6
LOC105379107	XR_001742832.1	n.619A>C		non_coding_transcript_exon_variant	Exon 3 of 3
LOC105379107	XR_001742833.2	n.759+21A>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.214 AC: 8893 AN: 41468

American (AMR) AF: 0.282 AC: 4305 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1214 AN: 3468

East Asian (EAS) AF: 0.159 AC: 822 AN: 5178

South Asian (SAS) AF: 0.309 AC: 1486 AN: 4802

European-Finnish (FIN) AF: 0.421 AC: 4441 AN: 10556

Middle Eastern (MID) AF: 0.394 AC: 115 AN: 292

European-Non Finnish (NFE) AF: 0.424 AC: 28814 AN: 67928

Other (OTH) AF: 0.349 AC: 737 AN: 2114

Alfa AF: 0.386 Hom.: 40935

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
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs1363258; hg19: chr5-103269694;