Variant rs7043482 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000637606.1(ENSG00000290551):n.985+24142A>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.486 in 151,962 control chromosomes in the GnomAD database, including 21,156 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 0.49 ( 21156 hom., cov: 32)

Failed GnomAD Quality Control

Consequence

ENST00000637606.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0150

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=-0.87).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107987087	XR_001746782.2 linkuse as main transcript	n.247+24142A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000637606.1 linkuse as main transcript	n.985+24142A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.485

AC:

73717

AN:

151844

Hom.:

21086

Cov.:

show subpopulations

Gnomad AFR

AF:

0.798

Gnomad AMI

AF:

0.324

Gnomad AMR

AF:

0.426

Gnomad ASJ

AF:

0.293

Gnomad EAS

AF:

0.664

Gnomad SAS

AF:

0.336

Gnomad FIN

AF:

0.374

Gnomad MID

AF:

0.399

Gnomad NFE

AF:

0.336

Gnomad OTH

AF:

0.464

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

GnomAD4 genome

AF:

0.486

AC:

73851

AN:

151962

Hom.:

21156

Cov.:

AF XY:

0.484

AC XY:

35951

AN XY:

74264

show subpopulations

Gnomad4 AFR

AF:

0.799

Gnomad4 AMR

AF:

0.427

Gnomad4 ASJ

AF:

0.293

Gnomad4 EAS

AF:

0.664

Gnomad4 SAS

AF:

0.335

Gnomad4 FIN

AF:

0.374

Gnomad4 NFE

AF:

0.336

Gnomad4 OTH

AF:

0.473

Alfa

AF:

0.357

Hom.:

20531

Bravo

AF:

0.509

Asia WGS

AF:

0.552

AC:

1919

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

2.2

DANN

Benign

0.74

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