Variant rs2307838 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000643167.1(ENSG00000234810):n.278+76625_278+76628del variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.45 ( 17097 hom., cov: 0)

Consequence

ENST00000643167.1 intron, non_coding_transcript

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.31

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Transcript	HGVSc	Effect	TSL
ENST00000643167.1 linkuse as main transcript	n.278+76625_278+76628del	intron_variant, non_coding_transcript_variant
ENST00000634769.1 linkuse as main transcript	n.274+76625_274+76628del	intron_variant, non_coding_transcript_variant	5
ENST00000646341.1 linkuse as main transcript	n.298+76625_298+76628del	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.450

AC:

68057

AN:

151372

Hom.:

17087

Cov.:

show subpopulations

Gnomad AFR

AF:

0.212

Gnomad AMI

AF:

0.556

Gnomad AMR

AF:

0.603

Gnomad ASJ

AF:

0.503

Gnomad EAS

AF:

0.309

Gnomad SAS

AF:

0.401

Gnomad FIN

AF:

0.515

Gnomad MID

AF:

0.462

Gnomad NFE

AF:

0.559

Gnomad OTH

AF:

0.485

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

GnomAD4 genome

AF:

0.449

AC:

68090

AN:

151490

Hom.:

17097

Cov.:

AF XY:

0.449

AC XY:

33236

AN XY:

74000

show subpopulations

Gnomad4 AFR

AF:

0.212

Gnomad4 AMR

AF:

0.603

Gnomad4 ASJ

AF:

0.503

Gnomad4 EAS

AF:

0.309

Gnomad4 SAS

AF:

0.403

Gnomad4 FIN

AF:

0.515

Gnomad4 NFE

AF:

0.559

Gnomad4 OTH

AF:

0.480

Alfa

AF:

0.492

Hom.:

2350

Bravo

AF:

0.449

Asia WGS

AF:

0.335

AC:

1164

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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