ENST00000722729.1:n.359-9981C>T

Variant names:

• chr15-94775998-G-A
• rs11073388
• ENST00000722729.1:n.359-9981C>T

Variant summary

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

The ENST00000722729.1(ENSG00000294319):​n.359-9981C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 152,042 control chromosomes in the GnomAD database, including 6,084 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 0.27 (6084 hom., cov: 33)
• Consequence: ENSG00000294319 ENST00000722729.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.227
• Publications: 4 publications found

Genes affected

ENSG00000294319 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000722729.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294319	ENST00000722729.1		n.359-9981C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.270 AC: 41056 AN: 151924 Hom.: 6088 Cov.: 33

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.270 AC: 41057 AN: 152042 Hom.: 6084 Cov.: 33 AF XY: 0.268 AC XY: 19893 AN XY: 74332

African (AFR) AF: 0.148 AC: 6132 AN: 41490

American (AMR) AF: 0.253 AC: 3861 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 891 AN: 3466

East Asian (EAS) AF: 0.390 AC: 2013 AN: 5160

South Asian (SAS) AF: 0.414 AC: 1995 AN: 4824

European-Finnish (FIN) AF: 0.238 AC: 2514 AN: 10572

Middle Eastern (MID) AF: 0.353 AC: 103 AN: 292

European-Non Finnish (NFE) AF: 0.332 AC: 22565 AN: 67952

Other (OTH) AF: 0.280 AC: 591 AN: 2112

Alfa AF: 0.314 Hom.: 9808

Bravo AF: 0.265

Asia WGS AF: 0.326 AC: 1134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.37
DANN	Benign	0.27
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs11073388; hg19: chr15-95319227;