rs3213875

Variant names:

• chr18-75472093-C-T
• rs3213875
• ENST00000715587.1:n.970-1339C>T

Variant summary

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

The ENST00000715587.1(ENSG00000287281):​n.970-1339C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 152,150 control chromosomes in the GnomAD database, including 11,258 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 0.38 (11258 hom., cov: 32)
• Consequence: ENSG00000287281 ENST00000715587.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.120
• Publications: 1 publications found

Genes affected

ENSG00000287281 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715587.1. 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
	ENSG00000287281	ENST00000715587.1		n.970-1339C>T		intron	N/A
	ENSG00000287281	ENST00000747310.1		n.1028-1339C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58285 AN: 152032 Hom.: 11250 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.383 AC: 58310 AN: 152150 Hom.: 11258 Cov.: 32 AF XY: 0.387 AC XY: 28796 AN XY: 74392

African (AFR) AF: 0.344 AC: 14274 AN: 41492

American (AMR) AF: 0.348 AC: 5323 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1551 AN: 3470

East Asian (EAS) AF: 0.448 AC: 2314 AN: 5164

South Asian (SAS) AF: 0.461 AC: 2221 AN: 4814

European-Finnish (FIN) AF: 0.449 AC: 4756 AN: 10594

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26601 AN: 68000

Other (OTH) AF: 0.419 AC: 886 AN: 2116

Alfa AF: 0.380 Hom.: 4241

Bravo AF: 0.372

Asia WGS AF: 0.446 AC: 1549 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.6
DANN	Benign	0.51
PhyloP100		0.12

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: rs3213875;

hg19: chr18-73184048;