7-132687774-C-T

Position:

• chr7-132687774-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_046323.1(FLJ40288):​n.407+25692C>T variant causes a intron, non coding transcript 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 NR_046323.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.800

Genes affected

FLJ40288 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FLJ40288	NR_046323.1	n.407+25692C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FLJ40288	ENST00000332558.8	n.407+25692C>T		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.679

Gnomad4 EAS AF: 0.701

Gnomad4 SAS AF: 0.651

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.630

Gnomad4 OTH AF: 0.523

Alfa AF: 0.582 Hom.: 15184

Bravo AF: 0.489

Asia WGS AF: 0.647 AC: 2252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.7
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs665506; hg19: chr7-132372533;