3-86797628-G-T

Variant names:

• chr3-86797628-G-T
• rs1437049
• ENST00000760372.1:n.236-1864G>T

Variant summary

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

The ENST00000760372.1(ENSG00000299083):​n.236-1864G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 151,880 control chromosomes in the GnomAD database, including 15,780 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 0.45 (15780 hom., cov: 32)
• Consequence: ENSG00000299083 ENST00000760372.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.820
• Publications: 4 publications found

Genes affected

ENSG00000299083 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.615 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
ENSG00000299083	ENST00000760372.1	n.236-1864G>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67556 AN: 151762 Hom.: 15751 Cov.: 32

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.445 AC: 67622 AN: 151880 Hom.: 15780 Cov.: 32 AF XY: 0.445 AC XY: 33014 AN XY: 74204

African (AFR) AF: 0.557 AC: 23064 AN: 41420

American (AMR) AF: 0.516 AC: 7864 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1027 AN: 3470

East Asian (EAS) AF: 0.633 AC: 3260 AN: 5152

South Asian (SAS) AF: 0.387 AC: 1864 AN: 4820

European-Finnish (FIN) AF: 0.353 AC: 3714 AN: 10530

Middle Eastern (MID) AF: 0.325 AC: 95 AN: 292

European-Non Finnish (NFE) AF: 0.375 AC: 25476 AN: 67930

Other (OTH) AF: 0.450 AC: 947 AN: 2104

Alfa AF: 0.442 Hom.: 3707

Bravo AF: 0.465

Asia WGS AF: 0.531 AC: 1845 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.15
DANN	Benign	0.23
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs1437049; hg19: chr3-86846778;