chr13-64317065-T-C

Variant names:

• chr13-64317065-T-C
• rs11148643
• XR_007063923.1:n.153-5294T>C

Variant summary

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

The XR_007063923.1(LOC124903237):​n.153-5294T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.459 in 151,854 control chromosomes in the GnomAD database, including 16,454 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 0.46 (16454 hom., cov: 32)
• Consequence: LOC124903237 XR_007063923.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.184
• Publications: 4 publications found

Genes affected

LOC124903237 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.521 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: 0.459 AC: 69626 AN: 151736 Hom.: 16427 Cov.: 32

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.459 AC: 69711 AN: 151854 Hom.: 16454 Cov.: 32 AF XY: 0.453 AC XY: 33589 AN XY: 74186

African (AFR) AF: 0.521 AC: 21574 AN: 41424

American (AMR) AF: 0.531 AC: 8085 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.422 AC: 1465 AN: 3470

East Asian (EAS) AF: 0.236 AC: 1216 AN: 5148

South Asian (SAS) AF: 0.398 AC: 1913 AN: 4808

European-Finnish (FIN) AF: 0.303 AC: 3199 AN: 10562

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.453 AC: 30774 AN: 67904

Other (OTH) AF: 0.460 AC: 971 AN: 2110

Alfa AF: 0.450 Hom.: 12623

Bravo AF: 0.479

Asia WGS AF: 0.380 AC: 1318 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.46
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs11148643; hg19: chr13-64891197;