Variant 7-110414465-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000658032.1(ENSG00000226965):n.331-49175G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 151,972 control chromosomes in the GnomAD database, including 19,290 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 0.50 ( 19290 hom., cov: 33)

Consequence

ENSG00000226965
ENST00000658032.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.29

Variant links:

Genes affected

ENSG00000226965 (HGNC:):

ENSG00000226965 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=-0.99).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.608 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375451	XR_927863.3 link	n.386+18346G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect
ENSG00000226965	ENST00000658032.1 link	n.331-49175G>A	intron_variant
ENSG00000226965	ENST00000666128.1 link	n.97+18346G>A	intron_variant
ENSG00000226965	ENST00000667232.1 link	n.411+18346G>A	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.500

AC:

75919

AN:

151854

Hom.:

19255

Cov.:

show subpopulations

Gnomad AFR

AF:

0.552

Gnomad AMI

AF:

0.581

Gnomad AMR

AF:

0.494

Gnomad ASJ

AF:

0.485

Gnomad EAS

AF:

0.625

Gnomad SAS

AF:

0.594

Gnomad FIN

AF:

0.399

Gnomad MID

AF:

0.567

Gnomad NFE

AF:

0.468

Gnomad OTH

AF:

0.510

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

GnomAD4 genome

AF:

0.500

AC:

76005

AN:

151972

Hom.:

19290

Cov.:

AF XY:

0.501

AC XY:

37239

AN XY:

74286

show subpopulations

Gnomad4 AFR

AF:

0.552

Gnomad4 AMR

AF:

0.494

Gnomad4 ASJ

AF:

0.485

Gnomad4 EAS

AF:

0.626

Gnomad4 SAS

AF:

0.594

Gnomad4 FIN

AF:

0.399

Gnomad4 NFE

AF:

0.468

Gnomad4 OTH

AF:

0.512

Alfa

AF:

0.483

Hom.:

8490

Bravo

AF:

0.511

Asia WGS

AF:

0.617

AC:

2135

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

1.2

DANN

Benign

0.74

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