18-1898710-A-G

Variant names:

• chr18-1898710-A-G
• rs312986
• ENST00000584867.1:n.357+7654T>C

Variant summary

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

The ENST00000584867.1(ENSG00000263745):​n.357+7654T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 151,462 control chromosomes in the GnomAD database, including 8,816 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 0.34 (8816 hom., cov: 31)
• Consequence: ENSG00000263745 ENST00000584867.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.403
• Publications: 1 publications found

Genes affected

ENSG00000263745 (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 (AFR) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000584867.1. 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
	ENSG00000263745	ENST00000584867.1	TSL:2	n.357+7654T>C		intron	N/A
	ENSG00000263745	ENST00000585072.6	TSL:5	n.94+7843T>C		intron	N/A
	ENSG00000266602	ENST00000653094.1		n.526+26779A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50764 AN: 151344 Hom.: 8819 Cov.: 31

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.335 AC: 50796 AN: 151462 Hom.: 8816 Cov.: 31 AF XY: 0.333 AC XY: 24640 AN XY: 74016

African (AFR) AF: 0.361 AC: 14937 AN: 41368

American (AMR) AF: 0.258 AC: 3906 AN: 15144

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 968 AN: 3460

East Asian (EAS) AF: 0.108 AC: 558 AN: 5148

South Asian (SAS) AF: 0.278 AC: 1339 AN: 4820

European-Finnish (FIN) AF: 0.372 AC: 3923 AN: 10554

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.359 AC: 24261 AN: 67656

Other (OTH) AF: 0.287 AC: 604 AN: 2108

Alfa AF: 0.280 Hom.: 1248

Bravo AF: 0.322

Asia WGS AF: 0.180 AC: 626 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	1.8
DANN	Benign	0.40
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs312986; hg19: chr18-1898711;