rs2101155

Variant names:

• chr3-129200625-G-A
• rs2101155
• ENST00000691714.2:n.408+16153G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-129200625-G-A
• chr3-129200625-G-C

Variant summary

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

The ENST00000691714.2(ENSG00000289469):​n.408+16153G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.807 in 151,996 control chromosomes in the GnomAD database, including 53,546 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 0.81 (53546 hom., cov: 30)
• Consequence: ENSG00000289469 ENST00000691714.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.339

Genes affected

ENSG00000289469 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.967 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
ENSG00000289469	ENST00000691714.2	n.408+16153G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.807 AC: 122597 AN: 151878 Hom.: 53552 Cov.: 30

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.872

Gnomad ASJ AF: 0.959

Gnomad EAS AF: 0.886

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.955

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.973

Gnomad OTH AF: 0.848

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

GnomAD4 genome AF: 0.807 AC: 122618 AN: 151996 Hom.: 53546 Cov.: 30 AF XY: 0.810 AC XY: 60173 AN XY: 74310

Gnomad4 AFR AF: 0.438

Gnomad4 AMR AF: 0.872

Gnomad4 ASJ AF: 0.959

Gnomad4 EAS AF: 0.886

Gnomad4 SAS AF: 0.845

Gnomad4 FIN AF: 0.955

Gnomad4 NFE AF: 0.973

Gnomad4 OTH AF: 0.845

Alfa AF: 0.879 Hom.: 7275

Bravo AF: 0.784

Asia WGS AF: 0.831 AC: 2893 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.2
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2101155; hg19: chr3-128919468;