Genetic Variant ENSG00000260410:n.952-6C>T (chr16-84121084-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000563242.2(ENSG00000260410):n.952-6C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 151,898 control chromosomes in the GnomAD database, including 18,508 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 0.49 ( 18503 hom., cov: 32)

Exomes 𝑓: 0.50 ( 5 hom. )

Consequence

ENSG00000260410
ENST00000563242.2 splice_region, intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.281

Variant links:

Genes affected

ENSG00000260410 (HGNC:):

ENSG00000260410 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=-0.73).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000260410	ENST00000563242.2 link	n.952-6C>T		splice_region_variant, intron_variant	Intron 1 of 1	6

Frequencies

GnomAD3 genomes

AF:

0.492

AC:

74681

AN:

151732

Hom.:

18481

Cov.:

show subpopulations

Gnomad AFR

AF:

0.491

Gnomad AMI

AF:

0.566

Gnomad AMR

AF:

0.526

Gnomad ASJ

AF:

0.532

Gnomad EAS

AF:

0.657

Gnomad SAS

AF:

0.427

Gnomad FIN

AF:

0.502

Gnomad MID

AF:

0.551

Gnomad NFE

AF:

0.472

Gnomad OTH

AF:

0.514

GnomAD4 exome

AF:

0.500

AC:

AN:

Hom.:

Cov.:

AF XY:

0.533

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.500

Gnomad4 FIN exome

AF:

0.625

Gnomad4 NFE exome

AF:

0.500

Gnomad4 OTH exome

AF:

0.500

GnomAD4 genome

AF:

0.492

AC:

74750

AN:

151850

Hom.:

18503

Cov.:

AF XY:

0.494

AC XY:

36632

AN XY:

74186

show subpopulations

Gnomad4 AFR

AF:

0.490

Gnomad4 AMR

AF:

0.527

Gnomad4 ASJ

AF:

0.532

Gnomad4 EAS

AF:

0.658

Gnomad4 SAS

AF:

0.428

Gnomad4 FIN

AF:

0.502

Gnomad4 NFE

AF:

0.472

Gnomad4 OTH

AF:

0.511

Alfa

AF:

0.477

Hom.:

29104

Bravo

AF:

0.497

Asia WGS

AF:

0.516

AC:

1790

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

0.58

DANN

Benign

0.65

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