rs31745

Positions:

• chr5-141040639-C-T

Variant summary

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

The ENST00000689319.1(ENSG00000288892):​n.267G>A 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 0.16 in 152,136 control chromosomes in the GnomAD database, including 2,866 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 0.16 (2866 hom., cov: 32)
• Consequence: ENSG00000288892 ENST00000689319.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.562

Genes affected

ENSG00000288892 (HGNC:58114):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000288892	ENST00000689319.1	n.267G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24350 AN: 152018 Hom.: 2858 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.0756

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.0788

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0930

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.160 AC: 24396 AN: 152136 Hom.: 2866 Cov.: 32 AF XY: 0.157 AC XY: 11708 AN XY: 74368

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.0757

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.0788

Gnomad4 NFE AF: 0.0931

Gnomad4 OTH AF: 0.142

Alfa AF: 0.119 Hom.: 343

Bravo AF: 0.167

Asia WGS AF: 0.111 AC: 385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	10
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: rs31745; hg19: chr5-140420224;