Variant chr10-43912449-T-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000446107.1(ENSG00000227029):n.6T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.59 in 152,212 control chromosomes in the GnomAD database, including 26,639 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 0.59 ( 26586 hom., cov: 31)

Exomes 𝑓: 0.64 ( 53 hom. )

Consequence

ENST00000446107.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.48

Variant links:

Genes affected

(HGNC:):

links:

LINC00841 (HGNC:27430): (long intergenic non-protein coding RNA 841)

LINC00841 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=-1.03).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
LINC00841	NR_136147.1 linkuse as main transcript	n.191+2790T>G	intron_variant, non_coding_transcript_variant
LINC00841	NR_136148.1 linkuse as main transcript	n.48T>G	non_coding_transcript_exon_variant	1/2
LINC00841	NR_033846.2 linkuse as main transcript	n.191+2790T>G	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000446107.1 linkuse as main transcript	n.6T>G		non_coding_transcript_exon_variant	1/2	2
LINC00841	ENST00000660538.1 linkuse as main transcript	n.191+2790T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.590

AC:

89623

AN:

151834

Hom.:

26569

Cov.:

show subpopulations

Gnomad AFR

AF:

0.532

Gnomad AMI

AF:

0.573

Gnomad AMR

AF:

0.544

Gnomad ASJ

AF:

0.645

Gnomad EAS

AF:

0.611

Gnomad SAS

AF:

0.693

Gnomad FIN

AF:

0.683

Gnomad MID

AF:

0.693

Gnomad NFE

AF:

0.609

Gnomad OTH

AF:

0.597

GnomAD4 exome

AF:

0.641

AC:

168

AN:

262

Hom.:

Cov.:

AF XY:

0.644

AC XY:

112

AN XY:

174

show subpopulations

Gnomad4 AFR exome

AF:

0.500

Gnomad4 EAS exome

AF:

0.500

Gnomad4 FIN exome

AF:

0.610

Gnomad4 NFE exome

AF:

0.665

Gnomad4 OTH exome

AF:

0.667

GnomAD4 genome

AF:

0.590

AC:

89667

AN:

151950

Hom.:

26586

Cov.:

AF XY:

0.595

AC XY:

44192

AN XY:

74250

show subpopulations

Gnomad4 AFR

AF:

0.532

Gnomad4 AMR

AF:

0.543

Gnomad4 ASJ

AF:

0.645

Gnomad4 EAS

AF:

0.612

Gnomad4 SAS

AF:

0.692

Gnomad4 FIN

AF:

0.683

Gnomad4 NFE

AF:

0.609

Gnomad4 OTH

AF:

0.601

Alfa

AF:

0.596

Hom.:

3373

Bravo

AF:

0.569

Asia WGS

AF:

0.651

AC:

2264

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.28

DANN

Benign

0.47

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