11-81231337-A-C

Variant names:

• chr11-81231337-A-C
• rs4999939
• ENST00000671134.1:n.324-43539A>C

Variant summary

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

The ENST00000671134.1(ENSG00000287912):​n.324-43539A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 151,806 control chromosomes in the GnomAD database, including 23,485 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 0.53 (23485 hom., cov: 32)
• Consequence: ENSG00000287912 ENST00000671134.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.655

Genes affected

ENSG00000287912 (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 (EAS) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287912	ENST00000671134.1	n.324-43539A>C		intron_variant	Intron 2 of 4
ENSG00000287912	ENST00000671210.1	n.310-43539A>C		intron_variant	Intron 2 of 2
ENSG00000287912	ENST00000701193.1	n.114-43539A>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80295 AN: 151688 Hom.: 23428 Cov.: 32

Gnomad AFR AF: 0.735

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.530 AC: 80408 AN: 151806 Hom.: 23485 Cov.: 32 AF XY: 0.531 AC XY: 39370 AN XY: 74196

Gnomad4 AFR AF: 0.735

Gnomad4 AMR AF: 0.589

Gnomad4 ASJ AF: 0.442

Gnomad4 EAS AF: 0.937

Gnomad4 SAS AF: 0.487

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.397

Gnomad4 OTH AF: 0.548

Alfa AF: 0.400 Hom.: 9766

Bravo AF: 0.559

Asia WGS AF: 0.742 AC: 2578 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.5
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4999939; hg19: chr11-80942380;