rs2218220

chr9-21756090-C-T

Variant summary

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

The XR_001746563.3(LOC107987026):n.163+11735G>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 0.598 in 151,686 control chromosomes in the GnomAD database, including 28,316 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 0.60 (28316 hom., cov: 30)
• Consequence: LOC107987026 XR_001746563.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310

Genes affected

LOC107987026 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.775 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107987026	XR_001746563.3	n.163+11735G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.598 AC: 90643 AN: 151568 Hom.: 28260 Cov.: 30

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.598 AC: 90766 AN: 151686 Hom.: 28316 Cov.: 30 AF XY: 0.593 AC XY: 43924 AN XY: 74066

Gnomad4 AFR AF: 0.782

Gnomad4 AMR AF: 0.595

Gnomad4 ASJ AF: 0.520

Gnomad4 EAS AF: 0.698

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.515

Gnomad4 NFE AF: 0.517

Gnomad4 OTH AF: 0.570

Alfa AF: 0.527 Hom.: 11552

Bravo AF: 0.621

Asia WGS AF: 0.536 AC: 1861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	2.1
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2218220; hg19: chr9-21756089;