13-75024980-A-G

Variant names:

• chr13-75024980-A-G
• rs9600419
• XR_001749917.1:n.148+653T>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.148+653T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 151,658 control chromosomes in the GnomAD database, including 20,122 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 0.50 (20122 hom., cov: 29)
• Consequence: LOC107984620 XR_001749917.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.303
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.58 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: 0.500 AC: 75699 AN: 151540 Hom.: 20115 Cov.: 29

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.499 AC: 75737 AN: 151658 Hom.: 20122 Cov.: 29 AF XY: 0.499 AC XY: 36946 AN XY: 74090

African (AFR) AF: 0.305 AC: 12626 AN: 41338

American (AMR) AF: 0.555 AC: 8453 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.577 AC: 2005 AN: 3472

East Asian (EAS) AF: 0.564 AC: 2892 AN: 5126

South Asian (SAS) AF: 0.436 AC: 2088 AN: 4784

European-Finnish (FIN) AF: 0.586 AC: 6149 AN: 10496

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.585 AC: 39701 AN: 67920

Other (OTH) AF: 0.525 AC: 1105 AN: 2104

Alfa AF: 0.500 Hom.: 4224

Bravo AF: 0.492

Asia WGS AF: 0.527 AC: 1832 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.36
DANN	Benign	0.33
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs9600419; hg19: chr13-75599117;