rs1320547

Variant names:

• chr9-93957442-C-T
• rs1320547
• ENST00000453045.1:n.1036-71C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130
• Publications: 5 publications found

Genes affected

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

LOC124902216 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BARX1-DT	NR_144455.1	n.1036-71C>T		intron_variant	Intron 1 of 1
LOC124902216	XR_007061671.1	n.115+1802C>T		intron_variant	Intron 1 of 1
LOC124902216	XR_007061672.1	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	n.1036-71C>T		intron_variant	Intron 1 of 1	1
BARX1-DT	ENST00000454594.1	n.45-71C>T		intron_variant	Intron 1 of 2	3
BARX1-DT	ENST00000766964.1	n.162+1802C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.623 AC: 94715 AN: 151936 Hom.: 31155 Cov.: 32

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: 32 AN: 72 Hom.: 8 AF XY: 0.420 AC XY: 21 AN XY: 50

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AF: 0.250 AC: 1 AN: 4

Middle Eastern (MID) AF: 0.357 AC: 5 AN: 14

European-Non Finnish (NFE) AF: 0.478 AC: 22 AN: 46

Other (OTH) AF: 0.250 AC: 1 AN: 4

GnomAD4 genome AF: 0.624 AC: 94816 AN: 152054 Hom.: 31200 Cov.: 32 AF XY: 0.624 AC XY: 46411 AN XY: 74338

African (AFR) AF: 0.825 AC: 34246 AN: 41496

American (AMR) AF: 0.706 AC: 10798 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1819 AN: 3464

East Asian (EAS) AF: 0.643 AC: 3308 AN: 5144

South Asian (SAS) AF: 0.429 AC: 2068 AN: 4824

European-Finnish (FIN) AF: 0.570 AC: 6024 AN: 10576

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.508 AC: 34530 AN: 67938

Other (OTH) AF: 0.633 AC: 1335 AN: 2110

Alfa AF: 0.582 Hom.: 3517

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
PhyloP100		0.013

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1320547; hg19: chr9-96719724;