ENST00000682415.1:n.76-4288G>C

Variant names:

• chr3-46086150-G-C
• rs6767559
• ENST00000682415.1:n.76-4288G>C

Variant summary

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

The ENST00000682415.1(ENSG00000288703):​n.76-4288G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.838 in 152,222 control chromosomes in the GnomAD database, including 54,089 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 0.84 (54089 hom., cov: 33)
• Consequence: ENSG00000288703 ENST00000682415.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• Publications: 6 publications found

Genes affected

ENSG00000288703 (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 = 0.967 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000682415.1. 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
	ENSG00000288703	ENST00000682415.1		n.76-4288G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.838 AC: 127487 AN: 152104 Hom.: 54025 Cov.: 33

Gnomad AFR AF: 0.937

Gnomad AMI AF: 0.658

Gnomad AMR AF: 0.880

Gnomad ASJ AF: 0.836

Gnomad EAS AF: 0.989

Gnomad SAS AF: 0.916

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.876

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.849

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

GnomAD4 genome AF: 0.838 AC: 127611 AN: 152222 Hom.: 54089 Cov.: 33 AF XY: 0.842 AC XY: 62678 AN XY: 74406

African (AFR) AF: 0.937 AC: 38936 AN: 41544

American (AMR) AF: 0.881 AC: 13469 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.836 AC: 2902 AN: 3470

East Asian (EAS) AF: 0.989 AC: 5121 AN: 5176

South Asian (SAS) AF: 0.916 AC: 4428 AN: 4832

European-Finnish (FIN) AF: 0.797 AC: 8436 AN: 10586

Middle Eastern (MID) AF: 0.880 AC: 257 AN: 292

European-Non Finnish (NFE) AF: 0.760 AC: 51666 AN: 68006

Other (OTH) AF: 0.852 AC: 1797 AN: 2110

Alfa AF: 0.800 Hom.: 6091

Bravo AF: 0.849

Asia WGS AF: 0.954 AC: 3317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.32
DANN	Benign	0.29
PhyloP100		-1.9
PromoterAI		0.0023	Neutral

Splicing

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

Other links and lift over

dbSNP: rs6767559; hg19: chr3-46127642;