chr11-81263412-A-G

Position:

• chr11-81263412-A-G

Variant summary

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

The ENST00000701193.1(ENSG00000287912):​n.114-11464A>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 0.828 in 151,478 control chromosomes in the GnomAD database, including 51,979 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 0.83 (51979 hom., cov: 32)
• Consequence: ENST00000701193.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.780

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.946 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.114-11464A>G		intron_variant, non_coding_transcript_variant
	ENST00000671134.1	n.324-11464A>G		intron_variant, non_coding_transcript_variant
	ENST00000671210.1	n.310-11464A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.828 AC: 125304 AN: 151360 Hom.: 51943 Cov.: 32

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.871

Gnomad AMR AF: 0.847

Gnomad ASJ AF: 0.846

Gnomad EAS AF: 0.968

Gnomad SAS AF: 0.866

Gnomad FIN AF: 0.831

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.817

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

GnomAD4 genome AF: 0.828 AC: 125394 AN: 151478 Hom.: 51979 Cov.: 32 AF XY: 0.831 AC XY: 61465 AN XY: 74004

Gnomad4 AFR AF: 0.812

Gnomad4 AMR AF: 0.847

Gnomad4 ASJ AF: 0.846

Gnomad4 EAS AF: 0.968

Gnomad4 SAS AF: 0.865

Gnomad4 FIN AF: 0.831

Gnomad4 NFE AF: 0.818

Gnomad4 OTH AF: 0.815

Alfa AF: 0.824 Hom.: 23415

Bravo AF: 0.830

Asia WGS AF: 0.901 AC: 3118 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.53
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1458072; hg19: chr11-80974455;