Variant 17-49901622-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The variant allele was found at a frequency of 0.246 in 151,944 control chromosomes in the GnomAD database, including 4,753 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 0.25 ( 4753 hom., cov: 31)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0920

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.4).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.49901622C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.246

AC:

37409

AN:

151826

Hom.:

4750

Cov.:

show subpopulations

Gnomad AFR

AF:

0.265

Gnomad AMI

AF:

0.123

Gnomad AMR

AF:

0.234

Gnomad ASJ

AF:

0.218

Gnomad EAS

AF:

0.00887

Gnomad SAS

AF:

0.235

Gnomad FIN

AF:

0.210

Gnomad MID

AF:

0.351

Gnomad NFE

AF:

0.264

Gnomad OTH

AF:

0.275

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

GnomAD4 genome

AF:

0.246

AC:

37429

AN:

151944

Hom.:

4753

Cov.:

AF XY:

0.242

AC XY:

17967

AN XY:

74280

show subpopulations

Gnomad4 AFR

AF:

0.265

Gnomad4 AMR

AF:

0.234

Gnomad4 ASJ

AF:

0.218

Gnomad4 EAS

AF:

0.00909

Gnomad4 SAS

AF:

0.236

Gnomad4 FIN

AF:

0.210

Gnomad4 NFE

AF:

0.264

Gnomad4 OTH

AF:

0.272

Alfa

AF:

0.263

Hom.:

5409

Bravo

AF:

0.251

Asia WGS

AF:

0.139

AC:

485

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.40

CADD

Benign

DANN

Benign

0.80

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