rs4084415

Variant names:

• chr9-2705970-A-C
• rs4084415
• ENST00000768783.1:n.114-37909T>G

Variant summary

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

The ENST00000768783.1(ENSG00000286670):​n.114-37909T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.635 in 151,934 control chromosomes in the GnomAD database, including 31,236 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 0.63 (31236 hom., cov: 32)
• Consequence: ENSG00000286670 ENST00000768783.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 3 publications found

Genes affected

ENSG00000286670 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.759 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
ENSG00000286670	ENST00000768783.1	n.114-37909T>G		intron_variant	Intron 1 of 3
ENSG00000286670	ENST00000768784.1	n.156+25975T>G		intron_variant	Intron 1 of 3
ENSG00000286670	ENST00000768785.1	n.156+25975T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.634 AC: 96304 AN: 151818 Hom.: 31178 Cov.: 32

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.635 AC: 96422 AN: 151934 Hom.: 31236 Cov.: 32 AF XY: 0.635 AC XY: 47109 AN XY: 74244

African (AFR) AF: 0.750 AC: 31093 AN: 41436

American (AMR) AF: 0.694 AC: 10596 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.630 AC: 2185 AN: 3470

East Asian (EAS) AF: 0.779 AC: 4031 AN: 5172

South Asian (SAS) AF: 0.610 AC: 2940 AN: 4820

European-Finnish (FIN) AF: 0.564 AC: 5931 AN: 10516

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.553 AC: 37593 AN: 67956

Other (OTH) AF: 0.637 AC: 1338 AN: 2102

Alfa AF: 0.606 Hom.: 8216

Bravo AF: 0.653

Asia WGS AF: 0.701 AC: 2434 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.15
DANN	Benign	0.58
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4084415; hg19: chr9-2705970;