Variant 16-9569798-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 ENST00000634367.2(ENSG00000283003):n.574+3208C>T 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 0.393 in 151,928 control chromosomes in the GnomAD database, including 12,159 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 0.39 ( 12159 hom., cov: 32)

Consequence

ENST00000634367.2 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.987

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=-0.69).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
LOC101927026	XR_007064980.1 linkuse as main transcript	n.942+3208C>T	intron_variant, non_coding_transcript_variant
LOC101927026	XR_001752074.2 linkuse as main transcript	n.643+3208C>T	intron_variant, non_coding_transcript_variant
LOC101927026	XR_007064979.1 linkuse as main transcript	n.570+3208C>T	intron_variant, non_coding_transcript_variant

Ensembl

Transcript	HGVSc	Effect	TSL
ENST00000634367.2 linkuse as main transcript	n.574+3208C>T	intron_variant, non_coding_transcript_variant	5
ENST00000653393.2 linkuse as main transcript	n.649+3208C>T	intron_variant, non_coding_transcript_variant
ENST00000701200.1 linkuse as main transcript	n.575+3208C>T	intron_variant, non_coding_transcript_variant
ENST00000701702.1 linkuse as main transcript	n.1052+2799C>T	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.393

AC:

59631

AN:

151810

Hom.:

12153

Cov.:

show subpopulations

Gnomad AFR

AF:

0.278

Gnomad AMI

AF:

0.473

Gnomad AMR

AF:

0.492

Gnomad ASJ

AF:

0.475

Gnomad EAS

AF:

0.360

Gnomad SAS

AF:

0.392

Gnomad FIN

AF:

0.376

Gnomad MID

AF:

0.474

Gnomad NFE

AF:

0.440

Gnomad OTH

AF:

0.402

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

GnomAD4 genome

AF:

0.393

AC:

59655

AN:

151928

Hom.:

12159

Cov.:

AF XY:

0.392

AC XY:

29111

AN XY:

74248

show subpopulations

Gnomad4 AFR

AF:

0.278

Gnomad4 AMR

AF:

0.491

Gnomad4 ASJ

AF:

0.475

Gnomad4 EAS

AF:

0.359

Gnomad4 SAS

AF:

0.393

Gnomad4 FIN

AF:

0.376

Gnomad4 NFE

AF:

0.440

Gnomad4 OTH

AF:

0.407

Alfa

AF:

0.428

Hom.:

8505

Bravo

AF:

0.392

Asia WGS

AF:

0.408

AC:

1420

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.69

CADD

Benign

6.8

DANN

Benign

0.76

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