rs2422166

Variant names:

• chr2-118079100-C-T
• rs2422166
• ENST00000747789.1:n.231+8413G>A

Variant summary

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

The ENST00000747789.1(ENSG00000297418):​n.231+8413G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 148,304 control chromosomes in the GnomAD database, including 6,496 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 0.29 (6496 hom., cov: 27)
• Consequence: ENSG00000297418 ENST00000747789.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.327
• Publications: 2 publications found

Genes affected

ENSG00000297418 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000747789.1. 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
	ENSG00000297418	ENST00000747789.1		n.231+8413G>A		intron	N/A
	ENSG00000297418	ENST00000747790.1		n.104+9151G>A		intron	N/A
	ENSG00000297418	ENST00000747791.1		n.272-4547G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.286 AC: 42449 AN: 148186 Hom.: 6489 Cov.: 27

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.286 AC: 42480 AN: 148304 Hom.: 6496 Cov.: 27 AF XY: 0.283 AC XY: 20385 AN XY: 72050

African (AFR) AF: 0.369 AC: 14741 AN: 39942

American (AMR) AF: 0.209 AC: 3051 AN: 14592

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1020 AN: 3446

East Asian (EAS) AF: 0.139 AC: 706 AN: 5092

South Asian (SAS) AF: 0.273 AC: 1249 AN: 4572

European-Finnish (FIN) AF: 0.189 AC: 1895 AN: 10032

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 18866 AN: 67396

Other (OTH) AF: 0.271 AC: 553 AN: 2040

Alfa AF: 0.281 Hom.: 1729

Bravo AF: 0.289

Asia WGS AF: 0.222 AC: 774 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.3
DANN	Benign	0.54
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs2422166; hg19: chr2-118836676;