rs878815

Variant names:

• chr14-66025389-G-A
• rs878815
• ENST00000775253.1:n.124-36739C>T

Your query was ambiguous. Multiple possible variants found:

• chr14-66025389-G-A
• chr14-66025389-G-C
• chr14-66025389-G-T

Variant summary

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

The ENST00000775253.1(ENSG00000258847):​n.124-36739C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 152,142 control chromosomes in the GnomAD database, including 22,684 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 0.52 (22684 hom., cov: 33)
• Consequence: ENSG00000258847 ENST00000775253.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.385
• Publications: 3 publications found

Genes affected

ENSG00000258847 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.796 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
ENSG00000258847	ENST00000775253.1	n.124-36739C>T		intron_variant	Intron 1 of 3
ENSG00000258847	ENST00000775254.1	n.123-36739C>T		intron_variant	Intron 1 of 2
ENSG00000258847	ENST00000775255.1	n.237+14057C>T		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.515 AC: 78270 AN: 152024 Hom.: 22633 Cov.: 33

Gnomad AFR AF: 0.803

Gnomad AMI AF: 0.406

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.515 AC: 78382 AN: 152142 Hom.: 22684 Cov.: 33 AF XY: 0.515 AC XY: 38322 AN XY: 74372

African (AFR) AF: 0.803 AC: 33342 AN: 41516

American (AMR) AF: 0.451 AC: 6892 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1271 AN: 3468

East Asian (EAS) AF: 0.342 AC: 1768 AN: 5168

South Asian (SAS) AF: 0.429 AC: 2069 AN: 4824

European-Finnish (FIN) AF: 0.448 AC: 4741 AN: 10574

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.394 AC: 26803 AN: 67986

Other (OTH) AF: 0.470 AC: 993 AN: 2112

Alfa AF: 0.411 Hom.: 11144

Bravo AF: 0.525

Asia WGS AF: 0.439 AC: 1529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.6
DANN	Benign	0.56
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs878815; hg19: chr14-66492107;