rs924368

Variant names:

• chr7-132669589-C-T
• rs924368
• ENST00000332558.8:n.407+7507C>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+7507C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 152,004 control chromosomes in the GnomAD database, including 11,060 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 0.36 (11060 hom., cov: 32)
• Consequence: FLJ40288 ENST00000332558.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.374
• Publications: 4 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=-0.62).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.455 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+7507C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FLJ40288	ENST00000332558.8	TSL:2	n.407+7507C>T		intron	N/A
	FLJ40288	ENST00000573229.1	TSL:3	n.243-2347C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.362 AC: 55018 AN: 151886 Hom.: 11062 Cov.: 32

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.362 AC: 55011 AN: 152004 Hom.: 11060 Cov.: 32 AF XY: 0.362 AC XY: 26898 AN XY: 74284

African (AFR) AF: 0.201 AC: 8318 AN: 41470

American (AMR) AF: 0.301 AC: 4593 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1557 AN: 3472

East Asian (EAS) AF: 0.338 AC: 1737 AN: 5136

South Asian (SAS) AF: 0.300 AC: 1446 AN: 4818

European-Finnish (FIN) AF: 0.460 AC: 4862 AN: 10576

Middle Eastern (MID) AF: 0.479 AC: 140 AN: 292

European-Non Finnish (NFE) AF: 0.459 AC: 31229 AN: 67976

Other (OTH) AF: 0.372 AC: 786 AN: 2112

Alfa AF: 0.434 Hom.: 30147

Bravo AF: 0.347

Asia WGS AF: 0.311 AC: 1082 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	7.4
DANN	Benign	0.62
PhyloP100		0.37
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: rs924368;

hg19: chr7-132354348;