Genetic Variant ENSG00000287578:n.76-4817G>A (chr6-95928967-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000658251.1(ENSG00000287578):n.76-4817G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 151,982 control chromosomes in the GnomAD database, including 7,510 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 0.28 ( 7510 hom., cov: 31)

Consequence

ENSG00000287578
ENST00000658251.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.787

Variant links:

Genes affected

ENSG00000287578 (HGNC:):

ENSG00000287578 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=-0.97).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986626	XR_001744263.2 link	n.148-4817G>A		intron_variant	Intron 1 of 2
LOC107986626	XR_001744264.2 link	n.148-4817G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287578	ENST00000658251.1 link	n.76-4817G>A		intron_variant	Intron 1 of 2
ENSG00000287578	ENST00000668456.1 link	n.106-4817G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.284

AC:

43201

AN:

151864

Hom.:

7510

Cov.:

show subpopulations

Gnomad AFR

AF:

0.101

Gnomad AMI

AF:

0.358

Gnomad AMR

AF:

0.271

Gnomad ASJ

AF:

0.367

Gnomad EAS

AF:

0.105

Gnomad SAS

AF:

0.235

Gnomad FIN

AF:

0.347

Gnomad MID

AF:

0.386

Gnomad NFE

AF:

0.400

Gnomad OTH

AF:

0.316

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

GnomAD4 genome

AF:

0.284

AC:

43195

AN:

151982

Hom.:

7510

Cov.:

AF XY:

0.279

AC XY:

20700

AN XY:

74256

show subpopulations

Gnomad4 AFR

AF:

0.101

Gnomad4 AMR

AF:

0.271

Gnomad4 ASJ

AF:

0.367

Gnomad4 EAS

AF:

0.106

Gnomad4 SAS

AF:

0.235

Gnomad4 FIN

AF:

0.347

Gnomad4 NFE

AF:

0.400

Gnomad4 OTH

AF:

0.314

Alfa

AF:

0.367

Hom.:

4726

Bravo

AF:

0.271

Asia WGS

AF:

0.181

AC:

629

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

6.9

DANN

Benign

0.69

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