3-107988906-T-G

Variant names:

• chr3-107988906-T-G
• rs697957
• ENST00000773022.1:n.213-93T>G

Variant summary

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

The ENST00000773022.1(ENSG00000300627):​n.213-93T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.763 in 152,180 control chromosomes in the GnomAD database, including 44,788 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 0.76 (44788 hom., cov: 33)
• Consequence: ENSG00000300627 ENST00000773022.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.518
• Publications: 8 publications found

Genes affected

ENSG00000300627 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000773022.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300627	ENST00000773022.1		n.213-93T>G		intron	N/A
	ENSG00000300627	ENST00000773023.1		n.93-93T>G		intron	N/A
	ENSG00000300627	ENST00000773020.1		n.-84T>G		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.763 AC: 116046 AN: 152062 Hom.: 44729 Cov.: 33

Gnomad AFR AF: 0.828

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.802

Gnomad EAS AF: 0.925

Gnomad SAS AF: 0.900

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.766

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

GnomAD4 genome AF: 0.763 AC: 116169 AN: 152180 Hom.: 44788 Cov.: 33 AF XY: 0.767 AC XY: 57033 AN XY: 74390

African (AFR) AF: 0.829 AC: 34428 AN: 41538

American (AMR) AF: 0.709 AC: 10836 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.802 AC: 2786 AN: 3472

East Asian (EAS) AF: 0.925 AC: 4786 AN: 5176

South Asian (SAS) AF: 0.900 AC: 4343 AN: 4826

European-Finnish (FIN) AF: 0.759 AC: 8032 AN: 10578

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.713 AC: 48503 AN: 67982

Other (OTH) AF: 0.769 AC: 1627 AN: 2116

Alfa AF: 0.732 Hom.: 136742

Bravo AF: 0.761

Asia WGS AF: 0.905 AC: 3150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.18
DANN	Benign	0.64
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs697957; hg19: chr3-107707753;