rs3808986

Positions:

• chr11-130040689-C-A
• chr11-130040689-C-T

Variant summary

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

The ENST00000527151.2(ENSG00000255535):​n.325C>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 0.185 in 152,216 control chromosomes in the GnomAD database, including 5,221 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 0.18 (5221 hom., cov: 33)
  • Exomes 𝑓: 0.11 (0 hom.)
• Consequence: ENSG00000255535 ENST00000527151.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.57

Genes affected

ENSG00000255535 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.130040689C>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000255535	ENST00000527151.2	n.325C>A		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.184 AC: 28036 AN: 152022 Hom.: 5207 Cov.: 33

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.0551

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0441

Gnomad EAS AF: 0.0559

Gnomad SAS AF: 0.0535

Gnomad FIN AF: 0.0648

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0698

Gnomad OTH AF: 0.149

GnomAD4 exome AF: 0.105 AC: 8 AN: 76 Hom.: 0 Cov.: 0 AF XY: 0.0962 AC XY: 5 AN XY: 52

Gnomad4 AFR exome AF: 0.500

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.167

Gnomad4 NFE exome AF: 0.0714

Gnomad4 OTH exome AF: 0.167

GnomAD4 genome AF: 0.185 AC: 28096 AN: 152140 Hom.: 5221 Cov.: 33 AF XY: 0.181 AC XY: 13444 AN XY: 74386

Gnomad4 AFR AF: 0.481

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.0441

Gnomad4 EAS AF: 0.0563

Gnomad4 SAS AF: 0.0531

Gnomad4 FIN AF: 0.0648

Gnomad4 NFE AF: 0.0698

Gnomad4 OTH AF: 0.150

Alfa AF: 0.0925 Hom.: 1775

Bravo AF: 0.204

Asia WGS AF: 0.102 AC: 359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	3.2
DANN	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3808986; hg19: chr11-129910584;