11-81269845-A-G

Position:

• chr11-81269845-A-G

Variant summary

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

The ENST00000701193.1(ENSG00000287912):​n.114-5031A>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 0.309 in 151,690 control chromosomes in the GnomAD database, including 8,706 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 (8706 hom., cov: 32)
• Consequence: ENST00000701193.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.223

Genes affected

(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 = 0.714 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000701193.1	n.114-5031A>G		intron_variant, non_coding_transcript_variant
	ENST00000671134.1	n.324-5031A>G		intron_variant, non_coding_transcript_variant
	ENST00000671210.1	n.310-5031A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46811 AN: 151572 Hom.: 8697 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.309 AC: 46861 AN: 151690 Hom.: 8706 Cov.: 32 AF XY: 0.313 AC XY: 23243 AN XY: 74144

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.278

Gnomad4 EAS AF: 0.734

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.314

Alfa AF: 0.222 Hom.: 5536

Bravo AF: 0.326

Asia WGS AF: 0.534 AC: 1855 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	3.4
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7941624; hg19: chr11-80980888;