Variant chr8-2804227-C-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_168443.1(LOC105377785):n.539-359C>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0124 in 151,962 control chromosomes in the GnomAD database, including 23 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 0.012 ( 23 hom., cov: 33)

Consequence

LOC105377785
NR_168443.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.947

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=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0602 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377785	NR_168443.1 linkuse as main transcript	n.539-359C>G		intron_variant, non_coding_transcript_variant

Ensembl

Transcript	HGVSc	Effect	TSL
ENST00000654515.1 linkuse as main transcript	n.532-359C>G	intron_variant, non_coding_transcript_variant
ENST00000520024.1 linkuse as main transcript	n.177-359C>G	intron_variant, non_coding_transcript_variant	3
ENST00000662575.1 linkuse as main transcript	n.82-359C>G	intron_variant, non_coding_transcript_variant
ENST00000670600.1 linkuse as main transcript	n.539-359C>G	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.0124

AC:

1883

AN:

151844

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00378

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.00788

Gnomad ASJ

AF:

0.0159

Gnomad EAS

AF:

0.0660

Gnomad SAS

AF:

0.0404

Gnomad FIN

AF:

0.00570

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0136

Gnomad OTH

AF:

0.0120

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

GnomAD4 genome

AF:

0.0124

AC:

1889

AN:

151962

Hom.:

Cov.:

AF XY:

0.0127

AC XY:

941

AN XY:

74258

show subpopulations

Gnomad4 AFR

AF:

0.00376

Gnomad4 AMR

AF:

0.00787

Gnomad4 ASJ

AF:

0.0159

Gnomad4 EAS

AF:

0.0659

Gnomad4 SAS

AF:

0.0402

Gnomad4 FIN

AF:

0.00570

Gnomad4 NFE

AF:

0.0136

Gnomad4 OTH

AF:

0.0156

Alfa

AF:

0.0104

Hom.:

Bravo

AF:

0.0122

Asia WGS

AF:

0.0680

AC:

236

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

8.1

DANN

Benign

0.53

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