3-127181649-T-C

Variant names:

• chr3-127181649-T-C
• rs9827714
• ENST00000654542.1:n.85-14853A>G

Variant summary

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

The ENST00000654542.1(ENSG00000287784):​n.85-14853A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 152,126 control chromosomes in the GnomAD database, including 15,329 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 0.44 (15329 hom., cov: 33)
• Consequence: ENSG00000287784 ENST00000654542.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.873
• Publications: 3 publications found

Genes affected

ENSG00000287784 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.607 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
ENSG00000287784	ENST00000654542.1	n.85-14853A>G		intron_variant	Intron 1 of 1
ENSG00000300635	ENST00000773073.1	n.92+1353A>G		intron_variant	Intron 1 of 2
ENSG00000300635	ENST00000773074.1	n.88-765A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67278 AN: 152008 Hom.: 15313 Cov.: 33

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.443 AC: 67336 AN: 152126 Hom.: 15329 Cov.: 33 AF XY: 0.443 AC XY: 32910 AN XY: 74348

African (AFR) AF: 0.368 AC: 15274 AN: 41526

American (AMR) AF: 0.409 AC: 6256 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1887 AN: 3468

East Asian (EAS) AF: 0.583 AC: 3014 AN: 5166

South Asian (SAS) AF: 0.626 AC: 3018 AN: 4824

European-Finnish (FIN) AF: 0.384 AC: 4061 AN: 10578

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.476 AC: 32365 AN: 67954

Other (OTH) AF: 0.452 AC: 956 AN: 2114

Alfa AF: 0.474 Hom.: 14460

Bravo AF: 0.435

Asia WGS AF: 0.630 AC: 2195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.5
DANN	Benign	0.41
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs9827714; hg19: chr3-126900492;