Variant chr6-98136857-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000607032.1(ENSG00000271860):n.410+37587C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 148,960 control chromosomes in the GnomAD database, including 11,815 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 0.38 ( 11815 hom., cov: 31)

Consequence

ENSG00000271860
ENST00000607032.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.801

Variant links:

Genes affected

ENSG00000271860 (HGNC:):

ENSG00000271860 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=-0.83).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
ENSG00000271860	ENST00000606913.5 link	n.240+37587C>A	intron_variant	5
ENSG00000271860	ENST00000607032.1 link	n.410+37587C>A	intron_variant	3
ENSG00000271860	ENST00000607823.5 link	n.352+37587C>A	intron_variant	5

Frequencies

GnomAD3 genomes

AF:

0.384

AC:

57219

AN:

148856

Hom.:

11819

Cov.:

show subpopulations

Gnomad AFR

AF:

0.218

Gnomad AMI

AF:

0.442

Gnomad AMR

AF:

0.346

Gnomad ASJ

AF:

0.479

Gnomad EAS

AF:

0.396

Gnomad SAS

AF:

0.256

Gnomad FIN

AF:

0.483

Gnomad MID

AF:

0.544

Gnomad NFE

AF:

0.480

Gnomad OTH

AF:

0.393

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

GnomAD4 genome

AF:

0.384

AC:

57208

AN:

148960

Hom.:

11815

Cov.:

AF XY:

0.381

AC XY:

27726

AN XY:

72688

show subpopulations

Gnomad4 AFR

AF:

0.218

Gnomad4 AMR

AF:

0.346

Gnomad4 ASJ

AF:

0.479

Gnomad4 EAS

AF:

0.396

Gnomad4 SAS

AF:

0.257

Gnomad4 FIN

AF:

0.483

Gnomad4 NFE

AF:

0.480

Gnomad4 OTH

AF:

0.387

Alfa

AF:

0.00809

Hom.:

Bravo

AF:

0.371

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.37

DANN

Benign

0.20

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