chr13-78977159-C-T

Variant names:

• chr13-78977159-C-T
• rs4885589
• XR_942108.4:n.276+2486G>A

Variant summary

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

The XR_942108.4(LOC105370273):​n.276+2486G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 151,936 control chromosomes in the GnomAD database, including 24,069 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 0.56 (24069 hom., cov: 32)
• Consequence: LOC105370273 XR_942108.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.159
• Publications: 3 publications found

Genes affected

LOC105370273 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.560 AC: 85061 AN: 151818 Hom.: 24044 Cov.: 32

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.608

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.560 AC: 85126 AN: 151936 Hom.: 24069 Cov.: 32 AF XY: 0.564 AC XY: 41861 AN XY: 74240

African (AFR) AF: 0.623 AC: 25790 AN: 41410

American (AMR) AF: 0.490 AC: 7484 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.597 AC: 2070 AN: 3468

East Asian (EAS) AF: 0.459 AC: 2363 AN: 5144

South Asian (SAS) AF: 0.384 AC: 1851 AN: 4816

European-Finnish (FIN) AF: 0.636 AC: 6714 AN: 10558

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.544 AC: 36983 AN: 67968

Other (OTH) AF: 0.541 AC: 1141 AN: 2110

Alfa AF: 0.530 Hom.: 23954

Bravo AF: 0.561

Asia WGS AF: 0.407 AC: 1413 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.36
DANN	Benign	0.67
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs4885589; hg19: chr13-79551294;