3-54084090-G-C

Variant names:

• chr3-54084090-G-C
• rs1349205
• ENST00000666932.2:n.1188-25534C>G

Variant summary

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

The ENST00000666932.2(ENSG00000286353):​n.1188-25534C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 151,918 control chromosomes in the GnomAD database, including 10,592 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 0.36 (10592 hom., cov: 31)
• Consequence: ENSG00000286353 ENST00000666932.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30
• Publications: 2 publications found

Genes affected

ENSG00000286353 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000666932.2. 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
	ENSG00000286353	ENST00000666932.2		n.1188-25534C>G		intron	N/A
	ENSG00000286353	ENST00000790844.1		n.576+5966C>G		intron	N/A
	ENSG00000286353	ENST00000790845.1		n.570+5966C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54205 AN: 151796 Hom.: 10578 Cov.: 31

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.357 AC: 54255 AN: 151918 Hom.: 10592 Cov.: 31 AF XY: 0.357 AC XY: 26532 AN XY: 74244

African (AFR) AF: 0.228 AC: 9449 AN: 41446

American (AMR) AF: 0.320 AC: 4890 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 878 AN: 3470

East Asian (EAS) AF: 0.210 AC: 1084 AN: 5156

South Asian (SAS) AF: 0.319 AC: 1534 AN: 4804

European-Finnish (FIN) AF: 0.532 AC: 5607 AN: 10542

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.436 AC: 29612 AN: 67934

Other (OTH) AF: 0.333 AC: 701 AN: 2104

Alfa AF: 0.389 Hom.: 1491

Bravo AF: 0.335

Asia WGS AF: 0.267 AC: 933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	12
DANN	Benign	0.78
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs1349205; hg19: chr3-54118117;