chr13-75027287-T-G

Variant names:

• chr13-75027287-T-G
• rs4885263
• XR_001749917.1:n.-200A>C

Variant summary

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

The XR_001749917.1(LOC107984620):​n.-200A>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.482 in 152,012 control chromosomes in the GnomAD database, including 19,304 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 0.48 (19304 hom., cov: 33)
• Consequence: LOC107984620 XR_001749917.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0690
• Publications: 2 publications found

Genes affected

LOC107984620 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73194 AN: 151894 Hom.: 19298 Cov.: 33

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.617

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.482 AC: 73227 AN: 152012 Hom.: 19304 Cov.: 33 AF XY: 0.481 AC XY: 35726 AN XY: 74268

African (AFR) AF: 0.254 AC: 10527 AN: 41466

American (AMR) AF: 0.547 AC: 8352 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1922 AN: 3472

East Asian (EAS) AF: 0.540 AC: 2786 AN: 5164

South Asian (SAS) AF: 0.429 AC: 2066 AN: 4818

European-Finnish (FIN) AF: 0.586 AC: 6185 AN: 10558

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.583 AC: 39592 AN: 67956

Other (OTH) AF: 0.512 AC: 1081 AN: 2112

Alfa AF: 0.497 Hom.: 4150

Bravo AF: 0.472

Asia WGS AF: 0.509 AC: 1767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.0
DANN	Benign	0.50
PhyloP100		-0.069

Splicing

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

Other links and lift over

dbSNP: rs4885263; hg19: chr13-75601424;