rs3886275

Variant names:

• chr2-57746209-A-C
• rs3886275
• ENST00000811253.1:n.148+36084T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000811253.1(ENSG00000285755):​n.148+36084T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.628 in 151,792 control chromosomes in the GnomAD database, including 29,848 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 0.63 (29848 hom., cov: 31)
• Consequence: ENSG00000285755 ENST00000811253.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.376
• Publications: 3 publications found

Genes affected

ENSG00000285755 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.627 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
ENSG00000285755	ENST00000811253.1	n.148+36084T>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.628 AC: 95226 AN: 151674 Hom.: 29826 Cov.: 31

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.740

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.650

Gnomad MID AF: 0.653

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.628 AC: 95294 AN: 151792 Hom.: 29848 Cov.: 31 AF XY: 0.626 AC XY: 46386 AN XY: 74148

African (AFR) AF: 0.634 AC: 26241 AN: 41416

American (AMR) AF: 0.590 AC: 8997 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.650 AC: 2253 AN: 3466

East Asian (EAS) AF: 0.619 AC: 3182 AN: 5138

South Asian (SAS) AF: 0.575 AC: 2763 AN: 4808

European-Finnish (FIN) AF: 0.650 AC: 6853 AN: 10550

Middle Eastern (MID) AF: 0.668 AC: 195 AN: 292

European-Non Finnish (NFE) AF: 0.631 AC: 42822 AN: 67860

Other (OTH) AF: 0.623 AC: 1313 AN: 2106

Alfa AF: 0.613 Hom.: 3553

Bravo AF: 0.623

Asia WGS AF: 0.600 AC: 2090 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.86
DANN	Benign	0.34
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs3886275; hg19: chr2-57973344;