rs739718

Variant names:

• chr5-132537381-T-C
• rs739718
• ENST00000640655.2:c.-168-21903T>C

Your query was ambiguous. Multiple possible variants found:

• chr5-132537381-T-C
• chr5-132537381-T-G

Variant summary

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

The ENST00000640655.2(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 ENST00000640655.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17

Genes affected

ENSG00000283782 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283782	ENST00000640655.2	c.-168-21903T>C		intron_variant	Intron 2 of 25	5		ENSP00000491596.2

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

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.0754

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.232

Gnomad4 SAS AF: 0.0439

Gnomad4 FIN AF: 0.0402

Gnomad4 NFE AF: 0.0593

Gnomad4 OTH AF: 0.116

Alfa AF: 0.0693 Hom.: 242

Bravo AF: 0.124

Asia WGS AF: 0.135 AC: 470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs739718; hg19: chr5-131873073;