ENST00000584867.1:n.357+7654T>C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000263745 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000263745	ENST00000584867.1	n.357+7654T>C		intron_variant	Intron 4 of 5	2
ENSG00000263745	ENST00000585072.6	n.94+7843T>C		intron_variant	Intron 1 of 2	5
ENSG00000266602	ENST00000653094.1	n.526+26779A>G		intron_variant	Intron 5 of 5

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

Gnomad4 AFR AF: 0.361

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.280

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.372

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.287

Alfa AF: 0.277 Hom.: 1200

Bravo AF: 0.322

Asia WGS AF: 0.180 AC: 626 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs312986; hg19: chr18-1898711;