rs2706399

Variant names:

• chr5-132532010-A-G
• rs2706399
• ENST00000640655.2:c.-168-27274A>G

Variant summary

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

The ENST00000640655.2(ENSG00000283782):​c.-168-27274A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 151,946 control chromosomes in the GnomAD database, including 13,649 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 0.40 (13649 hom., cov: 31)
• Consequence: ENSG00000283782 ENST00000640655.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.09

Genes affected

ENSG00000283782 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.491 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.-168-27274A>G		intron_variant	Intron 2 of 25	5		ENSP00000491596.2

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60931 AN: 151828 Hom.: 13637 Cov.: 31

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.401 AC: 60962 AN: 151946 Hom.: 13649 Cov.: 31 AF XY: 0.404 AC XY: 30033 AN XY: 74278

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.500

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.459

Gnomad4 FIN AF: 0.500

Gnomad4 NFE AF: 0.489

Gnomad4 OTH AF: 0.403

Alfa AF: 0.466 Hom.: 27484

Bravo AF: 0.389

Asia WGS AF: 0.317 AC: 1104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.16
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2706399; hg19: chr5-131867702;