Variant chr5-61752940-T-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000507461.2(C5orf64):n.542+1170T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.746 in 152,176 control chromosomes in the GnomAD database, including 43,142 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 0.75 ( 43142 hom., cov: 32)

Consequence

C5orf64
ENST00000507461.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.72

Variant links:

Genes affected

C5orf64 (HGNC:26744): (long intergenic non-protein coding RNA 3122) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

C5orf64 links:

LOC124900983 (HGNC:):

LOC124900983 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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
LOC124900983	XR_007058782.1 link	n.301+1170T>A	intron_variant
LOC124900983	XR_007058783.1 link	n.408+2396T>A	intron_variant
LOC124900983	XR_007058784.1 link	n.201-2892T>A	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
C5orf64	ENST00000507461.2 link	n.542+1170T>A	intron_variant	4
C5orf64	ENST00000655479.2 link	n.450+2396T>A	intron_variant
C5orf64	ENST00000656556.1 link	n.515+1170T>A	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.746

AC:

113382

AN:

152058

Hom.:

43107

Cov.:

show subpopulations

Gnomad AFR

AF:

0.882

Gnomad AMI

AF:

0.724

Gnomad AMR

AF:

0.631

Gnomad ASJ

AF:

0.780

Gnomad EAS

AF:

0.435

Gnomad SAS

AF:

0.679

Gnomad FIN

AF:

0.706

Gnomad MID

AF:

0.791

Gnomad NFE

AF:

0.721

Gnomad OTH

AF:

0.756

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

GnomAD4 genome

AF:

0.746

AC:

113470

AN:

152176

Hom.:

43142

Cov.:

AF XY:

0.739

AC XY:

54934

AN XY:

74376

show subpopulations

Gnomad4 AFR

AF:

0.882

Gnomad4 AMR

AF:

0.630

Gnomad4 ASJ

AF:

0.780

Gnomad4 EAS

AF:

0.435

Gnomad4 SAS

AF:

0.679

Gnomad4 FIN

AF:

0.706

Gnomad4 NFE

AF:

0.721

Gnomad4 OTH

AF:

0.750

Alfa

AF:

0.735

Hom.:

5177

Bravo

AF:

0.743

Asia WGS

AF:

0.579

AC:

2016

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.034

DANN

Benign

0.33

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