rs2422166

chr2-118079100-C-T

Variant summary

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

The XR_001739662.3(LOC107985940):n.181+9151G>A variant causes a intron, non coding transcript 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: LOC107985940 XR_001739662.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.327

Genes affected

LOC107985940 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985940	XR_001739662.3	n.181+9151G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.271

Alfa AF: 0.297 Hom.: 836

Bravo AF: 0.289

Asia WGS AF: 0.222 AC: 774 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	2.3
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2422166; hg19: chr2-118836676;