Variant 11-65745636-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 variant allele was found at a frequency of 0.798 in 152,196 control chromosomes in the GnomAD database, including 49,341 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 0.80 ( 49334 hom., cov: 32)

Exomes 𝑓: 0.94 ( 7 hom. )

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.97

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=-1.0).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.65745636T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.798

AC:

121408

AN:

152062

Hom.:

49303

Cov.:

show subpopulations

Gnomad AFR

AF:

0.723

Gnomad AMI

AF:

0.805

Gnomad AMR

AF:

0.669

Gnomad ASJ

AF:

0.829

Gnomad EAS

AF:

0.583

Gnomad SAS

AF:

0.669

Gnomad FIN

AF:

0.875

Gnomad MID

AF:

0.831

Gnomad NFE

AF:

0.885

Gnomad OTH

AF:

0.805

GnomAD4 exome

AF:

0.938

AC:

AN:

Hom.:

AF XY:

1.00

AC XY:

AN XY:

show subpopulations

Gnomad4 FIN exome

AF:

1.00

Gnomad4 NFE exome

AF:

1.00

Gnomad4 OTH exome

AF:

0.500

GnomAD4 genome

AF:

0.798

AC:

121493

AN:

152180

Hom.:

49334

Cov.:

AF XY:

0.792

AC XY:

58948

AN XY:

74390

show subpopulations

Gnomad4 AFR

AF:

0.723

Gnomad4 AMR

AF:

0.669

Gnomad4 ASJ

AF:

0.829

Gnomad4 EAS

AF:

0.582

Gnomad4 SAS

AF:

0.671

Gnomad4 FIN

AF:

0.875

Gnomad4 NFE

AF:

0.885

Gnomad4 OTH

AF:

0.807

Alfa

AF:

0.861

Hom.:

90869

Bravo

AF:

0.778

Asia WGS

AF:

0.646

AC:

2247

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.9

DANN

Benign

0.28

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