5-132537381-T-C

Variant names:

• chr5-132537381-T-C
• rs739718
• ENST00000638452.2:c.-168-21903T>C

Variant summary

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

The ENST00000638452.2(ENSG00000283782):​c.-168-21903T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,238 control chromosomes in the GnomAD database, including 1,499 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 0.11 (1499 hom., cov: 31)
• Consequence: ENSG00000283782 ENST00000638452.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17
• Publications: 25 publications found

Genes affected

ENSG00000283782 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000638452.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000283782	ENST00000638452.2	TSL:5	c.-168-21903T>C		intron	N/A	ENSP00000492349.2	A0A1W2PQ90
	ENSG00000283782	ENST00000638568.2	TSL:5	c.-310-18951T>C		intron	N/A	ENSP00000491158.2	A0A1W2PQ90
	ENSG00000283782	ENST00000640655.2	TSL:5	c.-168-21903T>C		intron	N/A	ENSP00000491596.2	A0A1W2PQ90

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17314 AN: 152120 Hom.: 1492 Cov.: 31

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0756

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.0445

Gnomad FIN AF: 0.0402

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.0593

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.114 AC: 17336 AN: 152238 Hom.: 1499 Cov.: 31 AF XY: 0.112 AC XY: 8346 AN XY: 74440

African (AFR) AF: 0.231 AC: 9580 AN: 41502

American (AMR) AF: 0.0754 AC: 1154 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 370 AN: 3472

East Asian (EAS) AF: 0.232 AC: 1205 AN: 5184

South Asian (SAS) AF: 0.0439 AC: 212 AN: 4828

European-Finnish (FIN) AF: 0.0402 AC: 427 AN: 10614

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.0593 AC: 4036 AN: 68020

Other (OTH) AF: 0.116 AC: 245 AN: 2114

Alfa AF: 0.0820 Hom.: 528

Bravo AF: 0.124

Asia WGS AF: 0.135 AC: 470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.7
DANN	Benign	0.71
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs739718; hg19: chr5-131873073;