ENST00000732860.1:n.88-14381G>A

Variant names:

• chr7-12448909-C-T
• rs4721099
• ENST00000732860.1:n.88-14381G>A

Variant summary

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

The ENST00000732860.1(ENSG00000295809):​n.88-14381G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0871 in 151,984 control chromosomes in the GnomAD database, including 785 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 0.087 (785 hom., cov: 32)
• Consequence: ENSG00000295809 ENST00000732860.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 3 publications found

Genes affected

ENSG00000295809 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000732860.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295809	ENST00000732860.1		n.88-14381G>A		intron	N/A
	ENSG00000295809	ENST00000732861.1		n.134-5100G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0872 AC: 13242 AN: 151866 Hom.: 787 Cov.: 32

Gnomad AFR AF: 0.0222

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.0669

Gnomad ASJ AF: 0.0798

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.0738

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

GnomAD4 genome AF: 0.0871 AC: 13232 AN: 151984 Hom.: 785 Cov.: 32 AF XY: 0.0881 AC XY: 6547 AN XY: 74298

African (AFR) AF: 0.0221 AC: 917 AN: 41500

American (AMR) AF: 0.0668 AC: 1018 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.0798 AC: 277 AN: 3470

East Asian (EAS) AF: 0.138 AC: 712 AN: 5178

South Asian (SAS) AF: 0.130 AC: 628 AN: 4822

European-Finnish (FIN) AF: 0.120 AC: 1267 AN: 10544

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8136 AN: 67908

Other (OTH) AF: 0.0730 AC: 154 AN: 2110

Alfa AF: 0.111 Hom.: 529

Bravo AF: 0.0804

Asia WGS AF: 0.113 AC: 390 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.3
DANN	Benign	0.72
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs4721099; hg19: chr7-12488535;