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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984620	XR_001749917.1	n.148+653T>C		intron_variant	Intron 2 of 3
LOC107984620	XR_001749918.1	n.99+2009T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;