rs4669584

Variant names:

• chr2-10437773-A-G
• rs4669584
• ENST00000757451.1:n.251+5529A>G

Variant summary

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

The ENST00000757451.1(ENSG00000298698):​n.251+5529A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,158 control chromosomes in the GnomAD database, including 3,998 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 0.22 (3998 hom., cov: 33)
• Consequence: ENSG00000298698 ENST00000757451.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280
• Publications: 1 publications found

Genes affected

ENSG00000298698 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.301 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
ENSG00000298698	ENST00000757451.1	n.251+5529A>G		intron_variant	Intron 1 of 1
ENSG00000298698	ENST00000757452.1	n.133-3669A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33260 AN: 152040 Hom.: 3967 Cov.: 33

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.0747

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.219 AC: 33344 AN: 152158 Hom.: 3998 Cov.: 33 AF XY: 0.225 AC XY: 16761 AN XY: 74374

African (AFR) AF: 0.306 AC: 12699 AN: 41514

American (AMR) AF: 0.153 AC: 2342 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 499 AN: 3472

East Asian (EAS) AF: 0.0745 AC: 386 AN: 5180

South Asian (SAS) AF: 0.303 AC: 1461 AN: 4820

European-Finnish (FIN) AF: 0.267 AC: 2817 AN: 10562

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12552 AN: 68006

Other (OTH) AF: 0.204 AC: 431 AN: 2112

Alfa AF: 0.204 Hom.: 1772

Bravo AF: 0.212

Asia WGS AF: 0.212 AC: 738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.8
DANN	Benign	0.61
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs4669584; hg19: chr2-10577899;