ENST00000584546.5:n.261-59C>T

Variant names:

• chr18-27501924-G-A
• rs1940989
• ENST00000584546.5:n.261-59C>T

Variant summary

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

The ENST00000584546.5(ENSG00000264151):​n.261-59C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0711 in 152,328 control chromosomes in the GnomAD database, including 482 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 0.071 (482 hom., cov: 32)
  • Exomes 𝑓: 0.050 (0 hom.)
• Consequence: ENSG00000264151 ENST00000584546.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 2 publications found

Genes affected

ENSG00000264151 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000584546.5. 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
	ENSG00000264151	ENST00000584546.5	TSL:2	n.261-59C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0711 AC: 10819 AN: 152170 Hom.: 486 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0834

Gnomad ASJ AF: 0.0841

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0366

Gnomad FIN AF: 0.0539

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0526

Gnomad OTH AF: 0.0871

GnomAD4 exome AF: 0.0500 AC: 2 AN: 40 Hom.: 0 AF XY: 0.0385 AC XY: 1 AN XY: 26

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 12

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0909 AC: 2 AN: 22

Other (OTH) AF: 0.00 AC: 0 AN: 6

GnomAD4 genome AF: 0.0711 AC: 10833 AN: 152288 Hom.: 482 Cov.: 32 AF XY: 0.0697 AC XY: 5189 AN XY: 74474

African (AFR) AF: 0.113 AC: 4696 AN: 41552

American (AMR) AF: 0.0835 AC: 1278 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0841 AC: 292 AN: 3470

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5180

South Asian (SAS) AF: 0.0367 AC: 177 AN: 4828

European-Finnish (FIN) AF: 0.0539 AC: 573 AN: 10624

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0527 AC: 3582 AN: 68018

Other (OTH) AF: 0.0862 AC: 182 AN: 2112

Alfa AF: 0.0627 Hom.: 581

Bravo AF: 0.0785

Asia WGS AF: 0.0240 AC: 84 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.71
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs1940989; hg19: chr18-25081888;