Variant rs10065575 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000644559.1(ENSG00000285190):n.720+5962G>A 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 0.477 in 151,374 control chromosomes in the GnomAD database, including 17,404 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 0.48 ( 17404 hom., cov: 29)

Consequence

ENST00000644559.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0340

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=-0.94).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105379066	XR_948543.1 linkuse as main transcript	n.80+5962G>A		intron_variant, non_coding_transcript_variant
LOC105379066	XR_948542.2 linkuse as main transcript	n.77+5962G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000644559.1 linkuse as main transcript	n.720+5962G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.476

AC:

72073

AN:

151256

Hom.:

17382

Cov.:

show subpopulations

Gnomad AFR

AF:

0.567

Gnomad AMI

AF:

0.454

Gnomad AMR

AF:

0.420

Gnomad ASJ

AF:

0.461

Gnomad EAS

AF:

0.509

Gnomad SAS

AF:

0.477

Gnomad FIN

AF:

0.454

Gnomad MID

AF:

0.583

Gnomad NFE

AF:

0.435

Gnomad OTH

AF:

0.494

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

GnomAD4 genome

AF:

0.477

AC:

72138

AN:

151374

Hom.:

17404

Cov.:

AF XY:

0.477

AC XY:

35274

AN XY:

73876

show subpopulations

Gnomad4 AFR

AF:

0.567

Gnomad4 AMR

AF:

0.419

Gnomad4 ASJ

AF:

0.461

Gnomad4 EAS

AF:

0.508

Gnomad4 SAS

AF:

0.479

Gnomad4 FIN

AF:

0.454

Gnomad4 NFE

AF:

0.435

Gnomad4 OTH

AF:

0.495

Alfa

AF:

0.438

Hom.:

19546

Bravo

AF:

0.480

Asia WGS

AF:

0.489

AC:

1699

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.84

DANN

Benign

0.36

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