Variant 17-49981460-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 variant allele was found at a frequency of 0.662 in 151,958 control chromosomes in the GnomAD database, including 37,435 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 0.66 ( 37435 hom., cov: 31)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.785

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=-0.56).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.818 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.49981460C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.663

AC:

100632

AN:

151840

Hom.:

37434

Cov.:

show subpopulations

Gnomad AFR

AF:

0.299

Gnomad AMI

AF:

0.814

Gnomad AMR

AF:

0.757

Gnomad ASJ

AF:

0.840

Gnomad EAS

AF:

0.705

Gnomad SAS

AF:

0.663

Gnomad FIN

AF:

0.812

Gnomad MID

AF:

0.671

Gnomad NFE

AF:

0.824

Gnomad OTH

AF:

0.699

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

GnomAD4 genome

AF:

0.662

AC:

100648

AN:

151958

Hom.:

37435

Cov.:

AF XY:

0.661

AC XY:

49064

AN XY:

74254

show subpopulations

Gnomad4 AFR

AF:

0.298

Gnomad4 AMR

AF:

0.758

Gnomad4 ASJ

AF:

0.840

Gnomad4 EAS

AF:

0.705

Gnomad4 SAS

AF:

0.664

Gnomad4 FIN

AF:

0.812

Gnomad4 NFE

AF:

0.824

Gnomad4 OTH

AF:

0.699

Alfa

AF:

0.780

Hom.:

48558

Bravo

AF:

0.644

Asia WGS

AF:

0.626

AC:

2175

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

4.4

DANN

Benign

0.81

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