11-3085429-C-T

Variant names:

• chr11-3085429-C-T
• rs2084239
• ENST00000431546.1:n.15G>A

Variant summary

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

The ENST00000431546.1(ENSG00000236710):​n.15G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 152,186 control chromosomes in the GnomAD database, including 9,854 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 0.32 (9853 hom., cov: 33)
  • Exomes 𝑓: 0.50 (1 hom.)
• Consequence: ENSG00000236710 ENST00000431546.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.320

Genes affected

ENSG00000236710 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.629 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
ENSG00000236710	ENST00000431546.1	n.15G>A		non_coding_transcript_exon_variant	Exon 1 of 2	6

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48857 AN: 152064 Hom.: 9837 Cov.: 33

Gnomad AFR AF: 0.0867

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.648

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.351

GnomAD4 exome AF: 0.500 AC: 2 AN: 4 Hom.: 1 Cov.: 0 AF XY: 0.500 AC XY: 2 AN XY: 4

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.321 AC: 48879 AN: 152182 Hom.: 9853 Cov.: 33 AF XY: 0.326 AC XY: 24248 AN XY: 74398

Gnomad4 AFR AF: 0.0865

Gnomad4 AMR AF: 0.480

Gnomad4 ASJ AF: 0.408

Gnomad4 EAS AF: 0.648

Gnomad4 SAS AF: 0.443

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.355

Alfa AF: 0.386 Hom.: 15660

Bravo AF: 0.322

Asia WGS AF: 0.522 AC: 1813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2084239; hg19: chr11-3106659;