5-116897540-T-C

Variant names:

• chr5-116897540-T-C
• rs2112342
• ENST00000795992.1:n.278-240A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000795992.1(ENSG00000303596):​n.278-240A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.654 in 151,844 control chromosomes in the GnomAD database, including 32,658 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 0.65 (32658 hom., cov: 31)
• Consequence: ENSG00000303596 ENST00000795992.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.182
• Publications: 1 publications found

Genes affected

ENSG00000303596 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.768 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
ENSG00000303596	ENST00000795992.1	n.278-240A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99180 AN: 151726 Hom.: 32607 Cov.: 31

Gnomad AFR AF: 0.709

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.788

Gnomad SAS AF: 0.771

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.685

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.654 AC: 99296 AN: 151844 Hom.: 32658 Cov.: 31 AF XY: 0.652 AC XY: 48351 AN XY: 74196

African (AFR) AF: 0.710 AC: 29411 AN: 41432

American (AMR) AF: 0.623 AC: 9501 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.698 AC: 2422 AN: 3468

East Asian (EAS) AF: 0.788 AC: 4067 AN: 5158

South Asian (SAS) AF: 0.771 AC: 3708 AN: 4808

European-Finnish (FIN) AF: 0.534 AC: 5600 AN: 10492

Middle Eastern (MID) AF: 0.688 AC: 201 AN: 292

European-Non Finnish (NFE) AF: 0.626 AC: 42510 AN: 67928

Other (OTH) AF: 0.660 AC: 1393 AN: 2110

Alfa AF: 0.640 Hom.: 130108

Bravo AF: 0.663

Asia WGS AF: 0.774 AC: 2692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.2
DANN	Benign	0.45
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs2112342; hg19: chr5-116233236;