rs11123469

chr2-118086607-T-C

Variant summary

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

The XR_001739662.3(LOC107985940):n.181+1644A>G 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 0.141 in 152,226 control chromosomes in the GnomAD database, including 1,834 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 0.14 (1834 hom., cov: 33)
• Consequence: LOC107985940 XR_001739662.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76

Genes affected

LOC107985940 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985940	XR_001739662.3	n.181+1644A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21387 AN: 152108 Hom.: 1834 Cov.: 33

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.0822

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0881

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.141 AC: 21397 AN: 152226 Hom.: 1834 Cov.: 33 AF XY: 0.140 AC XY: 10394 AN XY: 74408

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.0822

Gnomad4 NFE AF: 0.0881

Gnomad4 OTH AF: 0.122

Alfa AF: 0.131 Hom.: 347

Bravo AF: 0.156

Asia WGS AF: 0.196 AC: 681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.0050
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11123469; hg19: chr2-118844183;