rs31757

Variant names:

• chr5-166078230-G-A
• rs31757
• ENST00000752879.1:n.95-5518G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000752879.1(ENSG00000298087):​n.95-5518G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0751 in 152,144 control chromosomes in the GnomAD database, including 839 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 0.075 (839 hom., cov: 32)
• Consequence: ENSG00000298087 ENST00000752879.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.43
• Publications: 2 publications found

Genes affected

ENSG00000298087 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.192 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
ENSG00000298087	ENST00000752879.1	n.95-5518G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0749 AC: 11393 AN: 152026 Hom.: 837 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0353

Gnomad ASJ AF: 0.0268

Gnomad EAS AF: 0.0226

Gnomad SAS AF: 0.0336

Gnomad FIN AF: 0.00623

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0323

Gnomad OTH AF: 0.0621

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

GnomAD4 genome AF: 0.0751 AC: 11427 AN: 152144 Hom.: 839 Cov.: 32 AF XY: 0.0724 AC XY: 5380 AN XY: 74356

African (AFR) AF: 0.195 AC: 8109 AN: 41480

American (AMR) AF: 0.0352 AC: 538 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0268 AC: 93 AN: 3472

East Asian (EAS) AF: 0.0228 AC: 118 AN: 5174

South Asian (SAS) AF: 0.0334 AC: 161 AN: 4818

European-Finnish (FIN) AF: 0.00623 AC: 66 AN: 10588

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0323 AC: 2199 AN: 68012

Other (OTH) AF: 0.0624 AC: 132 AN: 2114

Alfa AF: 0.0669 Hom.: 102

Bravo AF: 0.0826

Asia WGS AF: 0.0390 AC: 134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	18
DANN	Benign	0.63
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs31757; hg19: chr5-165505235;