Variant chr13-64791868-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.518 in 151,968 control chromosomes in the GnomAD database, including 22,558 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 0.52 ( 22558 hom., cov: 32)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.46

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.64791868T>G		intergenic_region
LOC105370240	XR_942030.1 linkuse as main transcript	n.117-4315T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.519

AC:

78783

AN:

151850

Hom.:

22568

Cov.:

show subpopulations

Gnomad AFR

AF:

0.266

Gnomad AMI

AF:

0.558

Gnomad AMR

AF:

0.544

Gnomad ASJ

AF:

0.736

Gnomad EAS

AF:

0.758

Gnomad SAS

AF:

0.585

Gnomad FIN

AF:

0.655

Gnomad MID

AF:

0.586

Gnomad NFE

AF:

0.610

Gnomad OTH

AF:

0.563

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

GnomAD4 genome

AF:

0.518

AC:

78794

AN:

151968

Hom.:

22558

Cov.:

AF XY:

0.522

AC XY:

38792

AN XY:

74252

show subpopulations

Gnomad4 AFR

AF:

0.265

Gnomad4 AMR

AF:

0.544

Gnomad4 ASJ

AF:

0.736

Gnomad4 EAS

AF:

0.758

Gnomad4 SAS

AF:

0.585

Gnomad4 FIN

AF:

0.655

Gnomad4 NFE

AF:

0.610

Gnomad4 OTH

AF:

0.561

Alfa

AF:

0.599

Hom.:

37467

Bravo

AF:

0.498

Asia WGS

AF:

0.648

AC:

2251

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

DANN

Benign

0.79

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over