3-87734826-A-G

Variant names:

• chr3-87734826-A-G
• rs9860340
• ENST00000462792.2:n.418-3076T>C

Variant summary

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

The ENST00000462792.2(ENSG00000239572):​n.418-3076T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 152,062 control chromosomes in the GnomAD database, including 13,501 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 0.38 (13501 hom., cov: 32)
• Consequence: ENSG00000239572 ENST00000462792.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.09
• Publications: 5 publications found

Genes affected

ENSG00000239572 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377198	XR_941033.3	n.391-3076T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000239572	ENST00000462792.2	n.418-3076T>C		intron_variant	Intron 1 of 4	2
ENSG00000239572	ENST00000655850.1	n.406-3076T>C		intron_variant	Intron 1 of 2
ENSG00000239572	ENST00000667503.2	n.278-3076T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57086 AN: 151946 Hom.: 13463 Cov.: 32

Gnomad AFR AF: 0.670

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.376 AC: 57172 AN: 152062 Hom.: 13501 Cov.: 32 AF XY: 0.376 AC XY: 27925 AN XY: 74346

African (AFR) AF: 0.670 AC: 27783 AN: 41448

American (AMR) AF: 0.303 AC: 4627 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 666 AN: 3472

East Asian (EAS) AF: 0.426 AC: 2206 AN: 5180

South Asian (SAS) AF: 0.157 AC: 756 AN: 4824

European-Finnish (FIN) AF: 0.324 AC: 3426 AN: 10578

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16678 AN: 67978

Other (OTH) AF: 0.342 AC: 723 AN: 2112

Alfa AF: 0.289 Hom.: 18639

Bravo AF: 0.392

Asia WGS AF: 0.302 AC: 1050 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.13
DANN	Benign	0.11
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs9860340; hg19: chr3-87783976;