rs31746

Variant names:

• chr5-141040406-A-G
• rs31746
• ENST00000689319.1:n.500T>C

Variant summary

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

The ENST00000689319.1(ENSG00000288892):​n.500T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 152,000 control chromosomes in the GnomAD database, including 12,795 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 (12795 hom., cov: 32)
• Consequence: ENSG00000288892 ENST00000689319.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108

Genes affected

ENSG00000288892 (HGNC:58114):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.534 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
ENSG00000288892	ENST00000689319.1	n.500T>C		non_coding_transcript_exon_variant	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60264 AN: 151882 Hom.: 12764 Cov.: 32

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.397 AC: 60351 AN: 152000 Hom.: 12795 Cov.: 32 AF XY: 0.396 AC XY: 29444 AN XY: 74312

Gnomad4 AFR AF: 0.540

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.369

Gnomad4 EAS AF: 0.512

Gnomad4 SAS AF: 0.426

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.371

Alfa AF: 0.342 Hom.: 16430

Bravo AF: 0.412

Asia WGS AF: 0.437 AC: 1521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.8
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs31746; hg19: chr5-140419991;