7-132687774-C-T

Variant names:

• chr7-132687774-C-T
• rs665506
• ENST00000332558.8:n.407+25692C>T

Variant summary

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

The ENST00000332558.8(FLJ40288):​n.407+25692C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 152,034 control chromosomes in the GnomAD database, including 21,795 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 0.50 (21795 hom., cov: 32)
• Consequence: FLJ40288 ENST00000332558.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.800
• Publications: 6 publications found

Genes affected

FLJ40288 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000332558.8. 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
	FLJ40288	NR_046323.1		n.407+25692C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FLJ40288	ENST00000332558.8	TSL:2	n.407+25692C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76629 AN: 151916 Hom.: 21804 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.504 AC: 76638 AN: 152034 Hom.: 21795 Cov.: 32 AF XY: 0.505 AC XY: 37512 AN XY: 74312

African (AFR) AF: 0.232 AC: 9602 AN: 41460

American (AMR) AF: 0.491 AC: 7506 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.679 AC: 2354 AN: 3468

East Asian (EAS) AF: 0.701 AC: 3613 AN: 5156

South Asian (SAS) AF: 0.651 AC: 3129 AN: 4804

European-Finnish (FIN) AF: 0.535 AC: 5657 AN: 10568

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.630 AC: 42842 AN: 67964

Other (OTH) AF: 0.523 AC: 1106 AN: 2114

Alfa AF: 0.582 Hom.: 58425

Bravo AF: 0.489

Asia WGS AF: 0.647 AC: 2252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.7
DANN	Benign	0.38
PhyloP100		0.80
Mutation Taster		=100/0	polymorphism (auto)

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: rs665506;

hg19: chr7-132372533;