chr18-10447044-A-G

Variant names:

• chr18-10447044-A-G
• rs2847351
• ENST00000783284.1:n.123A>G

Variant summary

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

The ENST00000783284.1(ENSG00000301998):​n.123A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 151,974 control chromosomes in the GnomAD database, including 8,867 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 0.33 (8867 hom., cov: 32)
• Consequence: ENSG00000301998 ENST00000783284.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07
• Publications: 10 publications found

Genes affected

ENSG00000301998 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.492 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
ENSG00000301998	ENST00000783284.1	n.123A>G		non_coding_transcript_exon_variant	Exon 2 of 4

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50075 AN: 151856 Hom.: 8867 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.330 AC: 50093 AN: 151974 Hom.: 8867 Cov.: 32 AF XY: 0.341 AC XY: 25306 AN XY: 74268

African (AFR) AF: 0.222 AC: 9216 AN: 41458

American (AMR) AF: 0.420 AC: 6421 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1321 AN: 3468

East Asian (EAS) AF: 0.507 AC: 2603 AN: 5132

South Asian (SAS) AF: 0.509 AC: 2456 AN: 4828

European-Finnish (FIN) AF: 0.427 AC: 4506 AN: 10542

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.330 AC: 22457 AN: 67966

Other (OTH) AF: 0.338 AC: 710 AN: 2100

Alfa AF: 0.339 Hom.: 15777

Bravo AF: 0.324

Asia WGS AF: 0.503 AC: 1750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.6
DANN	Benign	0.85
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs2847351; hg19: chr18-10447041;