11-124901375-A-G

Position:

• chr11-124901375-A-G

Variant summary

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

The XR_001748429.3(LOC107984406):​n.334+9243A>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 0.272 in 151,850 control chromosomes in the GnomAD database, including 6,956 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 0.27 (6956 hom., cov: 31)
• Consequence: LOC107984406 XR_001748429.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.113

Genes affected

LOC107984406 (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 = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107984406	XR_001748429.3	n.334+9243A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41355 AN: 151730 Hom.: 6964 Cov.: 31

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.272 AC: 41336 AN: 151850 Hom.: 6956 Cov.: 31 AF XY: 0.265 AC XY: 19647 AN XY: 74226

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.00270

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.353

Gnomad4 NFE AF: 0.396

Gnomad4 OTH AF: 0.287

Alfa AF: 0.360 Hom.: 13710

Bravo AF: 0.257

Asia WGS AF: 0.0610 AC: 215 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	1.9
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4077566; hg19: chr11-124771271;