rs11227306

chr11-65811201-C-A

Variant summary

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

The XM_047427980.1(LOC124902693):c.*1058-7737G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 151,828 control chromosomes in the GnomAD database, including 7,924 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 0.31 (7924 hom., cov: 32)
• Consequence: LOC124902693 XM_047427980.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.402

Genes affected

LOC124902693 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902693	XM_047427980.1	c.*1058-7737G>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47680 AN: 151710 Hom.: 7907 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.314 AC: 47730 AN: 151828 Hom.: 7924 Cov.: 32 AF XY: 0.305 AC XY: 22661 AN XY: 74234

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.331

Gnomad4 EAS AF: 0.300

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.369

Gnomad4 OTH AF: 0.320

Alfa AF: 0.354 Hom.: 14242

Bravo AF: 0.317

Asia WGS AF: 0.236 AC: 822 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.7
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11227306; hg19: chr11-65578672;