rs3811699

Positions:

• chr3-49358927-T-C

Variant summary

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

The ENST00000704381.1(ENSG00000290318):​c.465-1180A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 151,910 control chromosomes in the GnomAD database, including 7,203 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 0.30 (7203 hom., cov: 31)
• Consequence: ENSG00000290318 ENST00000704381.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59

Genes affected

ENSG00000290318 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.49358927T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000290318	ENST00000704381.1	c.465-1180A>G		intron_variant				ENSP00000515884.1
ENSG00000290318	ENST00000704379.1	n.14A>G		non_coding_transcript_exon_variant	1/2
ENSG00000290318	ENST00000704380.1	n.85+130A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45157 AN: 151792 Hom.: 7196 Cov.: 31

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.0628

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.297 AC: 45186 AN: 151910 Hom.: 7203 Cov.: 31 AF XY: 0.300 AC XY: 22244 AN XY: 74252

Gnomad4 AFR AF: 0.293

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.461

Gnomad4 EAS AF: 0.0631

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.473

Gnomad4 NFE AF: 0.306

Gnomad4 OTH AF: 0.297

Alfa AF: 0.296 Hom.: 4266

Bravo AF: 0.278

Asia WGS AF: 0.152 AC: 535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.66
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3811699; hg19: chr3-49396360;