13-59548619-G-A

Variant names:

• chr13-59548619-G-A
• rs751531
• XR_001749886.2:n.234-17231C>T

Variant summary

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

The XR_001749886.2(LOC107984625):​n.234-17231C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0462 in 152,118 control chromosomes in the GnomAD database, including 416 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 0.046 (416 hom., cov: 32)
• Consequence: LOC107984625 XR_001749886.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.564
• Publications: 1 publications found

Genes affected

LOC107984625 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.265 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: 0.0462 AC: 7019 AN: 152000 Hom.: 414 Cov.: 32

Gnomad AFR AF: 0.0876

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0434

Gnomad ASJ AF: 0.00979

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0101

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00897

Gnomad OTH AF: 0.0311

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

GnomAD4 genome AF: 0.0462 AC: 7023 AN: 152118 Hom.: 416 Cov.: 32 AF XY: 0.0487 AC XY: 3620 AN XY: 74340

African (AFR) AF: 0.0875 AC: 3631 AN: 41498

American (AMR) AF: 0.0433 AC: 661 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.00979 AC: 34 AN: 3472

East Asian (EAS) AF: 0.276 AC: 1421 AN: 5140

South Asian (SAS) AF: 0.101 AC: 487 AN: 4814

European-Finnish (FIN) AF: 0.0101 AC: 107 AN: 10598

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.00897 AC: 610 AN: 68000

Other (OTH) AF: 0.0308 AC: 65 AN: 2110

Alfa AF: 0.00372 Hom.: 3

Bravo AF: 0.0502

Asia WGS AF: 0.153 AC: 533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.3
DANN	Benign	0.42
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs751531; hg19: chr13-60122753;