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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000462792.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000239572	ENST00000462792.2	TSL:2	n.418-3076T>C		intron	N/A
	ENSG00000239572	ENST00000655850.1		n.406-3076T>C		intron	N/A
	ENSG00000239572	ENST00000667503.2		n.278-3076T>C		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9860340;

hg19: chr3-87783976;