Variant chr16-85947995-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 ENST00000645383.1(ENSG00000285163):n.739T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.754 in 152,220 control chromosomes in the GnomAD database, including 44,264 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 0.75 ( 44256 hom., cov: 33)

Exomes 𝑓: 0.77 ( 8 hom. )

Consequence

ENSG00000285163
ENST00000645383.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.41

Variant links:

Genes affected

ENSG00000285163 (HGNC:):

ENSG00000285163 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=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.888 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105371388	XR_001752395.1 linkuse as main transcript	n.383T>C		non_coding_transcript_exon_variant	2/3

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons
ENSG00000285163	ENST00000645383.1 linkuse as main transcript	n.739T>C	non_coding_transcript_exon_variant	3/4
ENSG00000285163	ENST00000646214.1 linkuse as main transcript	n.423T>C	non_coding_transcript_exon_variant	3/4
ENSG00000285163	ENST00000646986.1 linkuse as main transcript	n.1061T>C	non_coding_transcript_exon_variant	3/4

Frequencies

GnomAD3 genomes

AF:

0.754

AC:

114625

AN:

152080

Hom.:

44190

Cov.:

show subpopulations

Gnomad AFR

AF:

0.895

Gnomad AMI

AF:

0.680

Gnomad AMR

AF:

0.731

Gnomad ASJ

AF:

0.600

Gnomad EAS

AF:

0.901

Gnomad SAS

AF:

0.782

Gnomad FIN

AF:

0.781

Gnomad MID

AF:

0.541

Gnomad NFE

AF:

0.667

Gnomad OTH

AF:

0.686

GnomAD4 exome

AF:

0.773

AC:

AN:

Hom.:

Cov.:

AF XY:

0.750

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

1.00

Gnomad4 FIN exome

AF:

0.500

Gnomad4 NFE exome

AF:

0.833

Gnomad4 OTH exome

AF:

1.00

GnomAD4 genome

AF:

0.754

AC:

114756

AN:

152198

Hom.:

44256

Cov.:

AF XY:

0.760

AC XY:

56518

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.896

Gnomad4 AMR

AF:

0.731

Gnomad4 ASJ

AF:

0.600

Gnomad4 EAS

AF:

0.902

Gnomad4 SAS

AF:

0.783

Gnomad4 FIN

AF:

0.781

Gnomad4 NFE

AF:

0.667

Gnomad4 OTH

AF:

0.690

Alfa

AF:

0.714

Hom.:

7926

Bravo

AF:

0.756

Asia WGS

AF:

0.855

AC:

2974

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.97

DANN

Benign

0.35

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