Variant chr6-78704977-T-A 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 0.208 in 152,160 control chromosomes in the GnomAD database, including 3,496 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 0.21 ( 3496 hom., cov: 32)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.353

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=-0.8).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.78704977T>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.209

AC:

31702

AN:

152042

Hom.:

3498

Cov.:

show subpopulations

Gnomad AFR

AF:

0.193

Gnomad AMI

AF:

0.0691

Gnomad AMR

AF:

0.211

Gnomad ASJ

AF:

0.148

Gnomad EAS

AF:

0.157

Gnomad SAS

AF:

0.133

Gnomad FIN

AF:

0.284

Gnomad MID

AF:

0.177

Gnomad NFE

AF:

0.220

Gnomad OTH

AF:

0.220

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

GnomAD4 genome

AF:

0.208

AC:

31714

AN:

152160

Hom.:

3496

Cov.:

AF XY:

0.212

AC XY:

15746

AN XY:

74386

show subpopulations

Gnomad4 AFR

AF:

0.193

Gnomad4 AMR

AF:

0.211

Gnomad4 ASJ

AF:

0.148

Gnomad4 EAS

AF:

0.156

Gnomad4 SAS

AF:

0.133

Gnomad4 FIN

AF:

0.284

Gnomad4 NFE

AF:

0.220

Gnomad4 OTH

AF:

0.217

Alfa

AF:

0.125

Hom.:

209

Bravo

AF:

0.203

Asia WGS

AF:

0.138

AC:

479

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

1.7

DANN

Benign

0.70

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