4-18864546-G-A

Variant names:

• chr4-18864546-G-A
• rs6845621
• ENST00000652661.1:n.988-13071G>A

Variant summary

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

The ENST00000652661.1(ENSG00000286046):​n.988-13071G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 151,748 control chromosomes in the GnomAD database, including 13,443 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 0.42 (13443 hom., cov: 31)
• Consequence: ENSG00000286046 ENST00000652661.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.93
• Publications: 4 publications found

Genes affected

ENSG00000286046 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652661.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286046	ENST00000652661.1		n.988-13071G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.419 AC: 63575 AN: 151630 Hom.: 13419 Cov.: 31

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.419 AC: 63652 AN: 151748 Hom.: 13443 Cov.: 31 AF XY: 0.422 AC XY: 31271 AN XY: 74128

African (AFR) AF: 0.387 AC: 16018 AN: 41384

American (AMR) AF: 0.475 AC: 7238 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.536 AC: 1859 AN: 3468

East Asian (EAS) AF: 0.547 AC: 2798 AN: 5118

South Asian (SAS) AF: 0.468 AC: 2253 AN: 4810

European-Finnish (FIN) AF: 0.382 AC: 4016 AN: 10526

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.414 AC: 28133 AN: 67890

Other (OTH) AF: 0.468 AC: 985 AN: 2104

Alfa AF: 0.423 Hom.: 25410

Bravo AF: 0.424

Asia WGS AF: 0.517 AC: 1800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.037
DANN	Benign	0.66
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs6845621; hg19: chr4-18866169;