rs924368

Positions:

• chr7-132669589-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+7507C>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 0.362 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 NR_046323.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.374

Genes affected

FLJ40288 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FLJ40288	NR_046323.1	n.407+7507C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FLJ40288	ENST00000332558.8	n.407+7507C>T		intron_variant, non_coding_transcript_variant		2
FLJ40288	ENST00000573229.1	n.243-2347C>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.301

Gnomad4 ASJ AF: 0.448

Gnomad4 EAS AF: 0.338

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.459

Gnomad4 OTH AF: 0.372

Alfa AF: 0.436 Hom.: 25770

Bravo AF: 0.347

Asia WGS AF: 0.311 AC: 1082 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	7.4
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs924368; hg19: chr7-132354348;