Variant chr18-10321513-T-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000666410.1(ENSG00000264876):n.1039-43A>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 0.453 in 152,060 control chromosomes in the GnomAD database, including 17,397 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 0.45 ( 17397 hom., cov: 32)

Consequence

ENST00000666410.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0480

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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
LOC105371985	XR_001753346.2 linkuse as main transcript	n.463+635A>G	intron_variant, non_coding_transcript_variant
LOC105371985	XR_001753344.2 linkuse as main transcript	n.532+635A>G	intron_variant, non_coding_transcript_variant
LOC105371985	XR_001753345.2 linkuse as main transcript	n.533-43A>G	intron_variant, non_coding_transcript_variant
LOC105371985	XR_007066287.1 linkuse as main transcript	n.432-43A>G	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000666410.1 linkuse as main transcript	n.1039-43A>G		intron_variant, non_coding_transcript_variant
	ENST00000669383.1 linkuse as main transcript	n.401-1510T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.453

AC:

68833

AN:

151942

Hom.:

17398

Cov.:

show subpopulations

Gnomad AFR

AF:

0.210

Gnomad AMI

AF:

0.476

Gnomad AMR

AF:

0.552

Gnomad ASJ

AF:

0.586

Gnomad EAS

AF:

0.683

Gnomad SAS

AF:

0.432

Gnomad FIN

AF:

0.539

Gnomad MID

AF:

0.563

Gnomad NFE

AF:

0.541

Gnomad OTH

AF:

0.477

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

GnomAD4 genome

AF:

0.453

AC:

68859

AN:

152060

Hom.:

17397

Cov.:

AF XY:

0.455

AC XY:

33813

AN XY:

74312

show subpopulations

Gnomad4 AFR

AF:

0.210

Gnomad4 AMR

AF:

0.552

Gnomad4 ASJ

AF:

0.586

Gnomad4 EAS

AF:

0.682

Gnomad4 SAS

AF:

0.432

Gnomad4 FIN

AF:

0.539

Gnomad4 NFE

AF:

0.541

Gnomad4 OTH

AF:

0.481

Alfa

AF:

0.500

Hom.:

9459

Bravo

AF:

0.448

Asia WGS

AF:

0.539

AC:

1874

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

3.0

DANN

Benign

0.60

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