dbSNP rs1320547: BARX1-DT:n.1036-71C>T (chr9-93957442-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000453045.1(BARX1-DT):n.1036-71C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.623 in 152,126 control chromosomes in the GnomAD database, including 31,208 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 0.62 ( 31200 hom., cov: 32)

Exomes 𝑓: 0.44 ( 8 hom. )

Consequence

BARX1-DT
ENST00000453045.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0130

Variant links:

Genes affected

BARX1-DT (HGNC:50673): (BARX1 divergent transcript)

BARX1-DT links:

LOC124902216 (HGNC:):

LOC124902216 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.818 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
BARX1-DT	NR_144455.1 link	n.1036-71C>T	intron_variant	Intron 1 of 1
LOC124902216	XR_007061671.1 link	n.115+1802C>T	intron_variant	Intron 1 of 1
LOC124902216	XR_007061672.1 link	n.115+1802C>T	intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BARX1-DT	ENST00000453045.1 link	n.1036-71C>T		intron_variant	Intron 1 of 1	1
BARX1-DT	ENST00000454594.1 link	n.45-71C>T		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes

AF:

0.623

AC:

94715

AN:

151936

Hom.:

31155

Cov.:

show subpopulations

Gnomad AFR

AF:

0.825

Gnomad AMI

AF:

0.563

Gnomad AMR

AF:

0.705

Gnomad ASJ

AF:

0.525

Gnomad EAS

AF:

0.644

Gnomad SAS

AF:

0.428

Gnomad FIN

AF:

0.570

Gnomad MID

AF:

0.604

Gnomad NFE

AF:

0.508

Gnomad OTH

AF:

0.636

GnomAD4 exome

AF:

0.444

AC:

AN:

Hom.:

AF XY:

0.420

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.500

Gnomad4 FIN exome

AF:

0.250

Gnomad4 NFE exome

AF:

0.478

Gnomad4 OTH exome

AF:

0.250

GnomAD4 genome

AF:

0.624

AC:

94816

AN:

152054

Hom.:

31200

Cov.:

AF XY:

0.624

AC XY:

46411

AN XY:

74338

show subpopulations

Gnomad4 AFR

AF:

0.825

Gnomad4 AMR

AF:

0.706

Gnomad4 ASJ

AF:

0.525

Gnomad4 EAS

AF:

0.643

Gnomad4 SAS

AF:

0.429

Gnomad4 FIN

AF:

0.570

Gnomad4 NFE

AF:

0.508

Gnomad4 OTH

AF:

0.633

Alfa

AF:

0.573

Hom.:

3265

Bravo

AF:

0.650

Asia WGS

AF:

0.544

AC:

1891

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.7

DANN

Benign

0.24

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