rs11834116

chr12-18782908-T-C

Variant summary

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

The XR_001749032.2(LOC102724227):n.654+9518T>C variant causes a intron, non coding transcript change. The variant allele was found at a frequency of 0.164 in 152,114 control chromosomes in the GnomAD database, including 2,269 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 0.16 (2269 hom., cov: 32)
• Consequence: LOC102724227 XR_001749032.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

Genes affected

LOC102724227 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102724227	XR_001749032.2	n.654+9518T>C		intron_variant, non_coding_transcript_variant
LOC102724227	XR_429054.4	n.654+9518T>C		intron_variant, non_coding_transcript_variant
LOC102724227	XR_931403.3	n.654+9518T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24956 AN: 151996 Hom.: 2261 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0462

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.164 AC: 24990 AN: 152114 Hom.: 2269 Cov.: 32 AF XY: 0.161 AC XY: 12000 AN XY: 74348

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.0460

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.164

Alfa AF: 0.123 Hom.: 661

Bravo AF: 0.162

Asia WGS AF: 0.0420 AC: 148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.40
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11834116; hg19: chr12-18935842;