Variant 11-1207997-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 0.366 in 152,120 control chromosomes in the GnomAD database, including 10,944 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 0.37 ( 10944 hom., cov: 33)

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.1207997C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.366

AC:

55608

AN:

152002

Hom.:

10928

Cov.:

show subpopulations

Gnomad AFR

AF:

0.509

Gnomad AMI

AF:

0.270

Gnomad AMR

AF:

0.429

Gnomad ASJ

AF:

0.294

Gnomad EAS

AF:

0.249

Gnomad SAS

AF:

0.322

Gnomad FIN

AF:

0.263

Gnomad MID

AF:

0.297

Gnomad NFE

AF:

0.299

Gnomad OTH

AF:

0.342

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

GnomAD4 genome

AF:

0.366

AC:

55673

AN:

152120

Hom.:

10944

Cov.:

AF XY:

0.365

AC XY:

27164

AN XY:

74336

show subpopulations

Gnomad4 AFR

AF:

0.509

Gnomad4 AMR

AF:

0.429

Gnomad4 ASJ

AF:

0.294

Gnomad4 EAS

AF:

0.250

Gnomad4 SAS

AF:

0.321

Gnomad4 FIN

AF:

0.263

Gnomad4 NFE

AF:

0.299

Gnomad4 OTH

AF:

0.339

Alfa

AF:

0.333

Hom.:

2416

Bravo

AF:

0.385

Asia WGS

AF:

0.327

AC:

1134

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.3

DANN

Benign

0.72

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