rs31746

Positions:

• chr5-141040406-A-G

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:):

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/exons	MANE	Protein	UniProt
		n.141040406A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000288892	ENST00000689319.1	n.500T>C		non_coding_transcript_exon_variant	1/1

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;