Variant 1-209248964-G-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000654974.1(ENSG00000232537):n.1457+11263C>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 0.843 in 151,856 control chromosomes in the GnomAD database, including 55,421 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 0.84 ( 55421 hom., cov: 30)

Consequence

ENST00000654974.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.133

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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.952 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372896	XR_922530.4 linkuse as main transcript	n.1458+11263C>G		intron_variant, non_coding_transcript_variant
LOC105372896	XR_922529.4 linkuse as main transcript	n.1458+11263C>G		intron_variant, non_coding_transcript_variant

Ensembl

Transcript	HGVSc	Effect
ENST00000654974.1 linkuse as main transcript	n.1457+11263C>G	intron_variant, non_coding_transcript_variant
ENST00000660754.1 linkuse as main transcript	n.74+11263C>G	intron_variant, non_coding_transcript_variant
ENST00000666483.1 linkuse as main transcript	n.53+11263C>G	intron_variant, non_coding_transcript_variant
ENST00000667236.1 linkuse as main transcript	n.53+11263C>G	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.843

AC:

127893

AN:

151738

Hom.:

55403

Cov.:

show subpopulations

Gnomad AFR

AF:

0.615

Gnomad AMI

AF:

0.992

Gnomad AMR

AF:

0.914

Gnomad ASJ

AF:

0.908

Gnomad EAS

AF:

0.974

Gnomad SAS

AF:

0.914

Gnomad FIN

AF:

0.938

Gnomad MID

AF:

0.930

Gnomad NFE

AF:

0.929

Gnomad OTH

AF:

0.865

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

GnomAD4 genome

AF:

0.843

AC:

127958

AN:

151856

Hom.:

55421

Cov.:

AF XY:

0.846

AC XY:

62743

AN XY:

74202

show subpopulations

Gnomad4 AFR

AF:

0.614

Gnomad4 AMR

AF:

0.915

Gnomad4 ASJ

AF:

0.908

Gnomad4 EAS

AF:

0.974

Gnomad4 SAS

AF:

0.914

Gnomad4 FIN

AF:

0.938

Gnomad4 NFE

AF:

0.929

Gnomad4 OTH

AF:

0.866

Alfa

AF:

0.878

Hom.:

7410

Bravo

AF:

0.831

Asia WGS

AF:

0.886

AC:

3081

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

5.2

DANN

Benign

0.55

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