rs11821466

Positions:

• chr11-106603534-A-G
• chr11-106603534-A-T

Variant summary

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

The ENST00000692272.1(ENSG00000289232):​n.222+639T>C 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 0.347 in 151,914 control chromosomes in the GnomAD database, including 11,736 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 0.35 (11736 hom., cov: 32)
• Consequence: ENST00000692272.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902744	XR_007062874.1	n.223+639T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000692272.1	n.222+639T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52658 AN: 151796 Hom.: 11695 Cov.: 32

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.0390

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.347 AC: 52762 AN: 151914 Hom.: 11736 Cov.: 32 AF XY: 0.345 AC XY: 25602 AN XY: 74240

Gnomad4 AFR AF: 0.631

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.0388

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.349

Gnomad4 NFE AF: 0.245

Gnomad4 OTH AF: 0.317

Alfa AF: 0.214 Hom.: 1377

Bravo AF: 0.356

Asia WGS AF: 0.124 AC: 432 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.068
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11821466; hg19: chr11-106474261;