rs4585146

Variant names:

• chr3-192100853-G-A
• rs4585146
• ENST00000653109.1:n.124+17930C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-192100853-G-A
• chr3-192100853-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000653109.1(ENSG00000287178):​n.124+17930C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 151,866 control chromosomes in the GnomAD database, including 7,816 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 0.31 (7816 hom., cov: 31)
• Consequence: ENSG00000287178 ENST00000653109.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50

Genes affected

ENSG00000287178 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.504 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
ENSG00000287178	ENST00000653109.1	n.124+17930C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46390 AN: 151748 Hom.: 7815 Cov.: 31

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.306 AC: 46401 AN: 151866 Hom.: 7816 Cov.: 31 AF XY: 0.307 AC XY: 22813 AN XY: 74202

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.355

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.521

Gnomad4 SAS AF: 0.301

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.337

Alfa AF: 0.351 Hom.: 9605

Bravo AF: 0.305

Asia WGS AF: 0.377 AC: 1306 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.30
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4585146; hg19: chr3-191818642;