NM_021570.4:c.224-559T>C

Variant names:

• chr9-93953746-A-G
• rs11789015
• NM_021570.4:c.224-559T>C

Variant summary

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

The NM_021570.4(BARX1):​c.224-559T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 152,148 control chromosomes in the GnomAD database, including 6,879 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 0.29 (6879 hom., cov: 34)
• Consequence: BARX1 NM_021570.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.366
• Publications: 36 publications found

Genes affected

BARX1 (HGNC:955): (BARX homeobox 1) This gene encodes a member of the Bar subclass of homeobox transcription factors. Studies of the mouse and chick homolog suggest the encoded protein may play a role in developing teeth and craniofacial mesenchyme of neural crest origin. The protein may also be associated with differentiation of stomach epithelia. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021570.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BARX1	NM_021570.4	MANE Select	c.224-559T>C		intron	N/A	NP_067545.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BARX1	ENST00000253968.11	TSL:1 MANE Select	c.224-559T>C		intron	N/A	ENSP00000253968.5

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44532 AN: 152030 Hom.: 6874 Cov.: 34

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.0851

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.293 AC: 44567 AN: 152148 Hom.: 6879 Cov.: 34 AF XY: 0.293 AC XY: 21801 AN XY: 74394

African (AFR) AF: 0.346 AC: 14371 AN: 41492

American (AMR) AF: 0.318 AC: 4863 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1133 AN: 3468

East Asian (EAS) AF: 0.0847 AC: 439 AN: 5184

South Asian (SAS) AF: 0.200 AC: 963 AN: 4824

European-Finnish (FIN) AF: 0.319 AC: 3376 AN: 10580

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.274 AC: 18633 AN: 67994

Other (OTH) AF: 0.289 AC: 610 AN: 2110

Alfa AF: 0.280 Hom.: 20991

Bravo AF: 0.294

Asia WGS AF: 0.144 AC: 500 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	11
DANN	Benign	0.46
PhyloP100		-0.37
PromoterAI		-0.036	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.080		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs11789015; hg19: chr9-96716028;