rs884618

Variant names:

• chr1-154628681-A-G
• rs884618
• ENST00000819301.1:n.68+614A>G

Variant summary

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

The ENST00000819301.1(ENSG00000306543):​n.68+614A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 152,186 control chromosomes in the GnomAD database, including 11,181 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 0.35 (11181 hom., cov: 33)
• Consequence: ENSG00000306543 ENST00000819301.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.712
• Publications: 16 publications found

Genes affected

ENSG00000306543 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000819301.1. 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
	ENSG00000306543	ENST00000819301.1		n.68+614A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.349 AC: 53138 AN: 152068 Hom.: 11181 Cov.: 33

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.349 AC: 53138 AN: 152186 Hom.: 11181 Cov.: 33 AF XY: 0.353 AC XY: 26230 AN XY: 74380

African (AFR) AF: 0.105 AC: 4356 AN: 41526

American (AMR) AF: 0.454 AC: 6947 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1557 AN: 3472

East Asian (EAS) AF: 0.513 AC: 2656 AN: 5180

South Asian (SAS) AF: 0.380 AC: 1837 AN: 4830

European-Finnish (FIN) AF: 0.427 AC: 4511 AN: 10574

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.440 AC: 29896 AN: 68004

Other (OTH) AF: 0.361 AC: 762 AN: 2108

Alfa AF: 0.414 Hom.: 6175

Bravo AF: 0.344

Asia WGS AF: 0.408 AC: 1419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	12
DANN	Benign	0.89
PhyloP100		0.71

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs884618;

hg19: chr1-154601157;