7-9684086-C-T

Variant names:

• chr7-9684086-C-T
• rs7805053
• ENST00000447999.2:n.272-23915C>T

Variant summary

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

The ENST00000447999.2(ENSG00000234710):​n.272-23915C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0591 in 151,956 control chromosomes in the GnomAD database, including 384 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 0.059 (384 hom., cov: 32)
• Consequence: ENSG00000234710 ENST00000447999.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357
• Publications: 3 publications found

Genes affected

ENSG00000234710 (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 = 0.0914 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000447999.2. 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
	LOC105375148	NR_187872.1		n.239-32704C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000234710	ENST00000447999.2	TSL:3	n.272-23915C>T		intron	N/A
	ENSG00000234710	ENST00000657272.2		n.280-32704C>T		intron	N/A
	ENSG00000234710	ENST00000731126.1		n.242-23915C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0591 AC: 8976 AN: 151838 Hom.: 383 Cov.: 32

Gnomad AFR AF: 0.0165

Gnomad AMI AF: 0.0516

Gnomad AMR AF: 0.0950

Gnomad ASJ AF: 0.0832

Gnomad EAS AF: 0.000777

Gnomad SAS AF: 0.0978

Gnomad FIN AF: 0.0345

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0812

Gnomad OTH AF: 0.0603

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

GnomAD4 genome AF: 0.0591 AC: 8983 AN: 151956 Hom.: 384 Cov.: 32 AF XY: 0.0586 AC XY: 4351 AN XY: 74258

African (AFR) AF: 0.0164 AC: 682 AN: 41494

American (AMR) AF: 0.0954 AC: 1458 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0832 AC: 288 AN: 3460

East Asian (EAS) AF: 0.000778 AC: 4 AN: 5140

South Asian (SAS) AF: 0.0981 AC: 473 AN: 4822

European-Finnish (FIN) AF: 0.0345 AC: 364 AN: 10544

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0812 AC: 5515 AN: 67904

Other (OTH) AF: 0.0597 AC: 126 AN: 2112

Alfa AF: 0.000916 Hom.: 28891

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.47
DANN	Benign	0.88
PhyloP100		-0.36

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7805053;

hg19: chr7-9723716;