2-122018889-C-T

Position:

• chr2-122018889-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000657880.1(ENSG00000286481):​n.603+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 ENST00000657880.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.916

Genes affected

ENSG00000286481 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373592	XR_001739684.2	n.651+74442C>T		intron_variant
LOC105373592	XR_001739685.2	n.651+74442C>T		intron_variant
LOC105373592	XR_007087222.1	n.651+74442C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000286481	ENST00000657880.1	n.603+74442C>T		intron_variant

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

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.0348

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.230

Alfa AF: 0.250 Hom.: 711

Bravo AF: 0.209

Asia WGS AF: 0.0900 AC: 317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17779391; hg19: chr2-122776465;