7-132682103-T-C

Variant names:

• chr7-132682103-T-C
• rs1364516
• ENST00000332558.8:n.407+20021T>C

Variant summary

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

The ENST00000332558.8(FLJ40288):​n.407+20021T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.669 in 152,024 control chromosomes in the GnomAD database, including 34,398 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 0.67 (34398 hom., cov: 32)
• Consequence: FLJ40288 ENST00000332558.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.624
• 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.705 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+20021T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FLJ40288	ENST00000332558.8	TSL:2	n.407+20021T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.669 AC: 101625 AN: 151906 Hom.: 34367 Cov.: 32

Gnomad AFR AF: 0.712

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.669 AC: 101710 AN: 152024 Hom.: 34398 Cov.: 32 AF XY: 0.667 AC XY: 49545 AN XY: 74300

African (AFR) AF: 0.712 AC: 29517 AN: 41462

American (AMR) AF: 0.548 AC: 8384 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.710 AC: 2462 AN: 3470

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

South Asian (SAS) AF: 0.677 AC: 3257 AN: 4808

European-Finnish (FIN) AF: 0.619 AC: 6537 AN: 10554

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.674 AC: 45789 AN: 67976

Other (OTH) AF: 0.662 AC: 1395 AN: 2106

Alfa AF: 0.653 Hom.: 10831

Bravo AF: 0.663

Asia WGS AF: 0.668 AC: 2327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.38
DANN	Benign	0.45
PhyloP100		-0.62
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: rs1364516;

hg19: chr7-132366862;