rs3808986

Variant names:

• chr11-130040689-C-A
• rs3808986
• ENST00000527151.2:n.325C>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

ENSG00000255535 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000527151.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000255535	ENST00000527151.2	TSL:6	n.325C>A		non_coding_transcript_exon	Exon 1 of 1

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

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.167 AC: 1 AN: 6

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.0714 AC: 4 AN: 56

Other (OTH) AF: 0.167 AC: 1 AN: 6

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

African (AFR) AF: 0.481 AC: 19947 AN: 41468

American (AMR) AF: 0.105 AC: 1610 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0441 AC: 153 AN: 3470

East Asian (EAS) AF: 0.0563 AC: 291 AN: 5172

South Asian (SAS) AF: 0.0531 AC: 256 AN: 4822

European-Finnish (FIN) AF: 0.0648 AC: 688 AN: 10614

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.0698 AC: 4744 AN: 68004

Other (OTH) AF: 0.150 AC: 315 AN: 2106

Alfa AF: 0.105 Hom.: 2983

Bravo AF: 0.204

Asia WGS AF: 0.102 AC: 359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	3.2
DANN	Benign	0.93
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs3808986; hg19: chr11-129910584;