ENST00000668609.2:n.1171-3519A>G

Variant names:

• chr2-18496421-T-C
• rs4119152
• ENST00000668609.2:n.1171-3519A>G

Variant summary

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

The ENST00000668609.2(ENSG00000287849):​n.1171-3519A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 152,132 control chromosomes in the GnomAD database, including 5,504 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 0.26 (5504 hom., cov: 32)
• Consequence: ENSG00000287849 ENST00000668609.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.292
• Publications: 3 publications found

Genes affected

ENSG00000287849 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373454	XR_001739302.1	n.815+3754T>C		intron_variant	Intron 5 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287849	ENST00000668609.2	n.1171-3519A>G		intron_variant	Intron 3 of 4
ENSG00000287881	ENST00000670548.1	n.197+3754T>C		intron_variant	Intron 2 of 2
ENSG00000287849	ENST00000690447.2	n.271-3519A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39108 AN: 152014 Hom.: 5506 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.0148

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.257 AC: 39118 AN: 152132 Hom.: 5504 Cov.: 32 AF XY: 0.249 AC XY: 18551 AN XY: 74366

African (AFR) AF: 0.202 AC: 8371 AN: 41510

American (AMR) AF: 0.211 AC: 3219 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1213 AN: 3466

East Asian (EAS) AF: 0.0146 AC: 76 AN: 5188

South Asian (SAS) AF: 0.155 AC: 750 AN: 4828

European-Finnish (FIN) AF: 0.246 AC: 2598 AN: 10570

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21885 AN: 67972

Other (OTH) AF: 0.255 AC: 539 AN: 2114

Alfa AF: 0.151 Hom.: 404

Bravo AF: 0.253

Asia WGS AF: 0.0900 AC: 313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.9
DANN	Benign	0.45
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs4119152; hg19: chr2-18677687;