Genetic Variant ENSG00000251095:n.1164C>T (chr4-89685446-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000612706.1(ENSG00000251095):n.1164C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.687 in 151,994 control chromosomes in the GnomAD database, including 36,316 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 0.69 ( 36314 hom., cov: 31)

Exomes 𝑓: 0.58 ( 2 hom. )

Consequence

ENSG00000251095
ENST00000612706.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0980

Variant links:

Genes affected

ENSG00000251095 (HGNC:):

ENSG00000251095 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=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC124900602	XR_001741764.2 link	n.3942C>T	non_coding_transcript_exon_variant	Exon 1 of 3
LOC124900602	XR_007058465.1 link	n.3942C>T	non_coding_transcript_exon_variant	Exon 1 of 2
LOC124900602	XR_007058466.1 link	n.3942C>T	non_coding_transcript_exon_variant	Exon 1 of 3
LOC124900602	XR_938983.2 link	n.3942C>T	non_coding_transcript_exon_variant	Exon 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000251095	ENST00000612706.1 link	n.1164C>T	non_coding_transcript_exon_variant	Exon 2 of 2	5
ENSG00000251095	ENST00000659714.1 link	n.700C>T	non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000251095	ENST00000506864.5 link	n.472-5839C>T	intron_variant	Intron 3 of 3	4

Frequencies

GnomAD3 genomes

AF:

0.687

AC:

104399

AN:

151864

Hom.:

36303

Cov.:

show subpopulations

Gnomad AFR

AF:

0.705

Gnomad AMI

AF:

0.676

Gnomad AMR

AF:

0.742

Gnomad ASJ

AF:

0.638

Gnomad EAS

AF:

0.983

Gnomad SAS

AF:

0.784

Gnomad FIN

AF:

0.677

Gnomad MID

AF:

0.668

Gnomad NFE

AF:

0.640

Gnomad OTH

AF:

0.662

GnomAD4 exome

AF:

0.583

AC:

AN:

Hom.:

Cov.:

AF XY:

0.600

AC XY:

AN XY:

show subpopulations

Gnomad4 NFE exome

AF:

0.583

GnomAD4 genome

AF:

0.687

AC:

104452

AN:

151982

Hom.:

36314

Cov.:

AF XY:

0.691

AC XY:

51316

AN XY:

74246

show subpopulations

Gnomad4 AFR

AF:

0.704

Gnomad4 AMR

AF:

0.743

Gnomad4 ASJ

AF:

0.638

Gnomad4 EAS

AF:

0.983

Gnomad4 SAS

AF:

0.782

Gnomad4 FIN

AF:

0.677

Gnomad4 NFE

AF:

0.640

Gnomad4 OTH

AF:

0.665

Alfa

AF:

0.628

Hom.:

8973

Bravo

AF:

0.692

Asia WGS

AF:

0.859

AC:

2984

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.7

DANN

Benign

0.62

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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