Variant 7-6374447-G-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 0.078 in 158,262 control chromosomes in the GnomAD database, including 1,177 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 0.078 ( 1105 hom., cov: 32)

Exomes 𝑓: 0.070 ( 72 hom. )

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.123

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=-0.48).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.6374447G>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.0782

AC:

11846

AN:

151490

Hom.:

1096

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0865

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.106

Gnomad ASJ

AF:

0.0640

Gnomad EAS

AF:

0.503

Gnomad SAS

AF:

0.206

Gnomad FIN

AF:

0.0920

Gnomad MID

AF:

0.0510

Gnomad NFE

AF:

0.0259

Gnomad OTH

AF:

0.0745

GnomAD4 exome

AF:

0.0698

AC:

465

AN:

6664

Hom.:

AF XY:

0.0639

AC XY:

239

AN XY:

3740

show subpopulations

Gnomad4 AFR exome

AF:

0.0588

Gnomad4 AMR exome

AF:

0.0960

Gnomad4 ASJ exome

AF:

0.0505

Gnomad4 EAS exome

AF:

0.524

Gnomad4 SAS exome

AF:

0.130

Gnomad4 FIN exome

AF:

0.0681

Gnomad4 NFE exome

AF:

0.0210

Gnomad4 OTH exome

AF:

0.0697

GnomAD4 genome

AF:

0.0784

AC:

11882

AN:

151598

Hom.:

1105

Cov.:

AF XY:

0.0879

AC XY:

6512

AN XY:

74094

show subpopulations

Gnomad4 AFR

AF:

0.0872

Gnomad4 AMR

AF:

0.105

Gnomad4 ASJ

AF:

0.0640

Gnomad4 EAS

AF:

0.504

Gnomad4 SAS

AF:

0.205

Gnomad4 FIN

AF:

0.0920

Gnomad4 NFE

AF:

0.0258

Gnomad4 OTH

AF:

0.0794

Alfa

AF:

0.0475

Hom.:

Bravo

AF:

0.0755

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.48

CADD

Benign

DANN

Benign

0.93

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