chr5-103933993-A-C

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.

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: 0.336 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 v4.9

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;