chr2-122018889-C-T

Variant names:

• chr2-122018889-C-T
• rs17779391
• ENST00000657880.2:n.654+74442C>T

Variant summary

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

The ENST00000657880.2(ENSG00000286481):​n.654+74442C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 152,148 control chromosomes in the GnomAD database, including 4,035 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 (4035 hom., cov: 32)
• Consequence: ENSG00000286481 ENST00000657880.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.916
• Publications: 3 publications found

Genes affected

ENSG00000286481 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000657880.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286481	ENST00000657880.2		n.654+74442C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33618 AN: 152030 Hom.: 4033 Cov.: 32

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.0351

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.221 AC: 33632 AN: 152148 Hom.: 4035 Cov.: 32 AF XY: 0.219 AC XY: 16257 AN XY: 74368

African (AFR) AF: 0.170 AC: 7071 AN: 41512

American (AMR) AF: 0.177 AC: 2709 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 950 AN: 3472

East Asian (EAS) AF: 0.0348 AC: 180 AN: 5170

South Asian (SAS) AF: 0.125 AC: 603 AN: 4814

European-Finnish (FIN) AF: 0.274 AC: 2892 AN: 10574

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18507 AN: 68004

Other (OTH) AF: 0.230 AC: 485 AN: 2108

Alfa AF: 0.246 Hom.: 718

Bravo AF: 0.209

Asia WGS AF: 0.0900 AC: 317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.63
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs17779391; hg19: chr2-122776465;