rs2888473

Variant names:

• chr14-85866945-A-T
• rs2888473
• ENST00000776545.1:n.150+1102T>A

Variant summary

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

The ENST00000776545.1(ENSG00000301142):​n.150+1102T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 152,158 control chromosomes in the GnomAD database, including 4,259 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 0.21 (4259 hom., cov: 33)
• Consequence: ENSG00000301142 ENST00000776545.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680
• Publications: 1 publications found

Genes affected

ENSG00000301142 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.299 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
ENSG00000301142	ENST00000776545.1	n.150+1102T>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31941 AN: 152040 Hom.: 4260 Cov.: 33

Gnomad AFR AF: 0.0529

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.210 AC: 31937 AN: 152158 Hom.: 4259 Cov.: 33 AF XY: 0.208 AC XY: 15490 AN XY: 74388

African (AFR) AF: 0.0527 AC: 2190 AN: 41558

American (AMR) AF: 0.186 AC: 2834 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 788 AN: 3470

East Asian (EAS) AF: 0.103 AC: 534 AN: 5174

South Asian (SAS) AF: 0.164 AC: 791 AN: 4822

European-Finnish (FIN) AF: 0.310 AC: 3284 AN: 10580

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.303 AC: 20573 AN: 67976

Other (OTH) AF: 0.225 AC: 475 AN: 2114

Alfa AF: 0.265 Hom.: 770

Bravo AF: 0.193

Asia WGS AF: 0.126 AC: 441 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.20
DANN	Benign	0.46
PhyloP100		0.068

Splicing

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

Other links and lift over

dbSNP: rs2888473; hg19: chr14-86333289;