rs4549225

Variant names:

• chr3-66717035-A-G
• rs4549225
• ENST00000735379.1:n.185+909T>C

Your query was ambiguous. Multiple possible variants found:

• chr3-66717035-A-G
• chr3-66717035-A-T

Variant summary

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

The ENST00000735379.1(ENSG00000296009):​n.185+909T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.66 in 152,120 control chromosomes in the GnomAD database, including 34,390 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 0.66 (34390 hom., cov: 33)
• Consequence: ENSG00000296009 ENST00000735379.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400
• Publications: 1 publications found

Genes affected

ENSG00000296009 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.857 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377142	XR_940935.3	n.185+909T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296009	ENST00000735379.1	n.185+909T>C		intron_variant	Intron 2 of 3
ENSG00000296009	ENST00000735381.1	n.288+15762T>C		intron_variant	Intron 2 of 2
ENSG00000296009	ENST00000735382.1	n.295+909T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.660 AC: 100371 AN: 152000 Hom.: 34349 Cov.: 33

Gnomad AFR AF: 0.864

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.653

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

GnomAD4 genome AF: 0.660 AC: 100462 AN: 152120 Hom.: 34390 Cov.: 33 AF XY: 0.658 AC XY: 48949 AN XY: 74358

African (AFR) AF: 0.864 AC: 35881 AN: 41528

American (AMR) AF: 0.587 AC: 8977 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.619 AC: 2149 AN: 3470

East Asian (EAS) AF: 0.601 AC: 3103 AN: 5166

South Asian (SAS) AF: 0.481 AC: 2317 AN: 4814

European-Finnish (FIN) AF: 0.598 AC: 6311 AN: 10562

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.584 AC: 39671 AN: 67978

Other (OTH) AF: 0.652 AC: 1376 AN: 2112

Alfa AF: 0.637 Hom.: 5198

Bravo AF: 0.673

Asia WGS AF: 0.531 AC: 1849 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.65
PhyloP100		0.040

Splicing

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

Other links and lift over

dbSNP: rs4549225; hg19: chr3-66767459;