Variant 5-57653695-T-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_104668.1(LOC101928505):n.100+2936T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.677 in 151,978 control chromosomes in the GnomAD database, including 35,079 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 0.68 ( 35079 hom., cov: 31)

Consequence

LOC101928505
NR_104668.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.74

Variant links:

Genes affected

ENSG00000287709 (HGNC:):

ENSG00000287709 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=-1.01).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101928505	NR_104668.1 link	n.100+2936T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect
ENSG00000287709	ENST00000661344.3 link	n.211+2826T>C	intron_variant
ENSG00000287709	ENST00000685494.1 link	n.104+2936T>C	intron_variant
ENSG00000287709	ENST00000688166.1 link	n.88+2936T>C	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.677

AC:

102786

AN:

151860

Hom.:

35019

Cov.:

show subpopulations

Gnomad AFR

AF:

0.726

Gnomad AMI

AF:

0.727

Gnomad AMR

AF:

0.606

Gnomad ASJ

AF:

0.621

Gnomad EAS

AF:

0.479

Gnomad SAS

AF:

0.624

Gnomad FIN

AF:

0.673

Gnomad MID

AF:

0.604

Gnomad NFE

AF:

0.685

Gnomad OTH

AF:

0.663

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

GnomAD4 genome

AF:

0.677

AC:

102916

AN:

151978

Hom.:

35079

Cov.:

AF XY:

0.673

AC XY:

49961

AN XY:

74228

show subpopulations

Gnomad4 AFR

AF:

0.727

Gnomad4 AMR

AF:

0.606

Gnomad4 ASJ

AF:

0.621

Gnomad4 EAS

AF:

0.478

Gnomad4 SAS

AF:

0.626

Gnomad4 FIN

AF:

0.673

Gnomad4 NFE

AF:

0.685

Gnomad4 OTH

AF:

0.665

Alfa

AF:

0.676

Hom.:

59089

Bravo

AF:

0.674

Asia WGS

AF:

0.603

AC:

2094

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.19

DANN

Benign

0.44

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