rs4890912

Variant names:

• chr18-77173985-G-A
• rs4890912
• ENST00000843890.1:n.300+11103G>A

Variant summary

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

The ENST00000843890.1(ENSG00000265844):​n.300+11103G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 152,086 control chromosomes in the GnomAD database, including 28,254 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 0.60 (28254 hom., cov: 33)
• Consequence: ENSG00000265844 ENST00000843890.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.265
• Publications: 3 publications found

Genes affected

ENSG00000265844 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.757 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000843890.1. 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
	ENSG00000265844	ENST00000843890.1		n.300+11103G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.600 AC: 91176 AN: 151968 Hom.: 28251 Cov.: 33

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.551

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.600 AC: 91200 AN: 152086 Hom.: 28254 Cov.: 33 AF XY: 0.603 AC XY: 44849 AN XY: 74358

African (AFR) AF: 0.444 AC: 18387 AN: 41458

American (AMR) AF: 0.567 AC: 8672 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.661 AC: 2292 AN: 3470

East Asian (EAS) AF: 0.777 AC: 4023 AN: 5176

South Asian (SAS) AF: 0.646 AC: 3118 AN: 4824

European-Finnish (FIN) AF: 0.711 AC: 7522 AN: 10580

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.665 AC: 45232 AN: 67980

Other (OTH) AF: 0.603 AC: 1275 AN: 2114

Alfa AF: 0.646 Hom.: 136467

Bravo AF: 0.588

Asia WGS AF: 0.685 AC: 2381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.14
DANN	Benign	0.43
PhyloP100		-0.27

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: rs4890912;

hg19: chr18-74885941;